From 3ee7195fa882683f5501ecdf60128f07c574b88c Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 12 Mar 2019 14:58:41 +0100 Subject: [PATCH 01/38] Central resource for both binac and cfc now --- conf/binac.config | 3 +-- conf/cfc.config | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/conf/binac.config b/conf/binac.config index 12da68d..a2ff5da 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -16,8 +16,7 @@ process { } params { - igenomesIgnore = false - igenomes_base = '/beegfs/work/igenomes' + igenomes_base = '/nfsmounts/igenomes' max_memory = 128.GB max_cpus = 28 max_time = 48.h diff --git a/conf/cfc.config b/conf/cfc.config index fc8cc34..2f31170 100644 --- a/conf/cfc.config +++ b/conf/cfc.config @@ -16,8 +16,7 @@ process { } params { - igenomesIgnore = false - igenomes_base = '/sfs/7/igenomes' + igenomes_base = '/nfsmounts/igenomes' max_memory = 60.GB max_cpus = 20 max_time = 140.h From a79564f0afc4e2d33351f6f2be48d7b2315bfd14 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 12 Mar 2019 17:02:24 +0100 Subject: [PATCH 02/38] Remove requirement for dev branch PRs --- .travis.yml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/.travis.yml b/.travis.yml index b200b4a..276304c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -9,10 +9,6 @@ cache: pip matrix: fast_finish: true -before_install: - # PRs to master are only ok if coming from dev branch - - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])' - install: # Install Nextflow - mkdir /tmp/nextflow && cd /tmp/nextflow @@ -26,4 +22,7 @@ env: script: # Run the pipeline with the test profile and test remote config - - grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | tr -s ' ' | cut -d " " -f 2 | xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile {} + - grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | \ + tr -s ' ' | \ + cut -d " " -f 2 | \ + xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile {} From eaa1c8360fc3fd6b76e3b1b5f5f8dc9ce4c625b4 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 12 Mar 2019 17:25:16 +0100 Subject: [PATCH 03/38] Travis multiline yaml --- .travis.yml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 276304c..918a846 100644 --- a/.travis.yml +++ b/.travis.yml @@ -22,7 +22,8 @@ env: script: # Run the pipeline with the test profile and test remote config - - grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | \ - tr -s ' ' | \ - cut -d " " -f 2 | \ - xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile {} + - | + grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | \ + tr -s ' ' | \ + cut -d " " -f 2 | \ + xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile {} From fbf9397182916186df308ea5ffedd261755b1fb2 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 12 Mar 2019 18:48:29 +0100 Subject: [PATCH 04/38] Bump --- conf/binac.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/binac.config b/conf/binac.config index a2ff5da..782071c 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -5,6 +5,7 @@ params { config_profile_contact = 'Alexander Peltzer (@apeltzer)' config_profile_url = 'https://www.bwhpc-c5.de/wiki/index.php/Category:BwForCluster_BinAC' } + singularity { enabled = true } From 1191863e1c03327c304e1e07925fc3a575806fc3 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 13 Mar 2019 17:15:16 +0100 Subject: [PATCH 05/38] Removed params.config_profile_name, added params.hostnames --- README.md | 9 ++++++++- conf/binac.config | 2 +- conf/ccga.config | 3 +-- conf/cfc.config | 1 - conf/crick.config | 3 +-- conf/gis.config | 15 ++++++--------- conf/hebbe.config | 3 +-- conf/mendel.config | 1 - conf/munin.config | 1 - conf/phoenix.config | 1 - conf/shh.config | 1 - conf/uct_hex.config | 2 -- conf/uppmax-devel.config | 1 - conf/uppmax.config | 1 - conf/uzh.config | 1 - nfcore_custom.config | 14 +++++++++++--- 16 files changed, 29 insertions(+), 30 deletions(-) diff --git a/README.md b/README.md index 6a53642..acb2ea4 100644 --- a/README.md +++ b/README.md @@ -58,7 +58,14 @@ nextflow run /path/to/pipeline/ -c /path/to/my/configs/configs-master/conf/my_co If you decide to upload your custom config file to `nf-core/configs` then this will ensure that your custom config file will be automatically downloaded, and available at run-time to all nf-core pipelines, and to everyone within your organisation. You will simply have to specify `-profile ` in the command used to run the pipeline. See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples. -Please also make sure to add an extra `params` section with `params. config_profile_name`, `params.config_profile_description`, `params.config_profile_contact` and `params.config_profile_url` set to reasonable values. Users will get information on who wrote the configuration profile then when executing a nf-core pipeline and can report back if there are things missing for example. +Please also make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` and `params.config_profile_url` set to reasonable values. Users will get information on who wrote the configuration profile then when executing a nf-core pipeline and can report back if there are things missing for example. + +## Checking user hostnames + +If your cluster has a set of consistent hostnames, nf-core pipelines can check that users are using your profile. +Add one or more hostname substrings to `params.hostnames` under a key that matches the profile name. +If the user's hostname contains this string at the start of a run or when a run fails and their profile +does not contain the profile name, a warning message will be printed. ### Testing diff --git a/conf/binac.config b/conf/binac.config index 12da68d..3cd1edc 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -1,10 +1,10 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'BINAC' config_profile_description = 'BINAC cluster profile provided by nf-core/configs.' config_profile_contact = 'Alexander Peltzer (@apeltzer)' config_profile_url = 'https://www.bwhpc-c5.de/wiki/index.php/Category:BwForCluster_BinAC' } + singularity { enabled = true } diff --git a/conf/ccga.config b/conf/ccga.config index 7dff7c7..f29db9c 100644 --- a/conf/ccga.config +++ b/conf/ccga.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'CCGA' config_profile_description = 'CCGA cluster profile provided by nf-core/configs.' config_profile_contact = 'Marc Hoeppner (@marchoeppner)' config_profile_url = 'https://www.ikmb.uni-kiel.de/' @@ -25,7 +24,7 @@ process { clusterOptions = { "--qos=ikmb_a" } } - + params { // illumina iGenomes reference file paths on RZCluster igenomes_base = '/ifs/data/nfs_share/ikmb_repository/references/iGenomes/references/' diff --git a/conf/cfc.config b/conf/cfc.config index fc8cc34..783e233 100644 --- a/conf/cfc.config +++ b/conf/cfc.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'CFC' config_profile_description = 'QBiC Core Facility cluster profile provided by nf-core/configs.' config_profile_contact = 'Alexander Peltzer (@apeltzer)' config_profile_url = 'http://qbic.uni-tuebingen.de/' diff --git a/conf/crick.config b/conf/crick.config index de8c89b..10ddba5 100755 --- a/conf/crick.config +++ b/conf/crick.config @@ -1,8 +1,7 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'CRICK' config_profile_description = 'The Francis Crick Institute CAMP HPC cluster profile provided by nf-core/configs.' - config_profile_contact = 'Harshil Patel (@drpatelh )' + config_profile_contact = 'Harshil Patel (@drpatelh)' config_profile_url = 'https://www.crick.ac.uk/research/platforms-and-facilities/scientific-computing/technologies' } diff --git a/conf/gis.config b/conf/gis.config index 3fcb72e..e1645e5 100644 --- a/conf/gis.config +++ b/conf/gis.config @@ -1,11 +1,9 @@ -/* - * ------------------------------------------------- - * Nextflow config file for GIS (Aquila) - * ------------------------------------------------- - * Defines reference genomes, using iGenome paths - * Imported under the default 'standard' Nextflow - * profile in nextflow.config - */ +//Profile config names for nf-core/configs +params { + config_profile_description = 'Genome Institute of Singapore (Aquila) cluster profile provided by nf-core/configs.' + config_profile_contact = 'Andreas Wilm (@andreas-wilm)' + config_profile_url = 'https://www.a-star.edu.sg/gis/' +} process { executor = 'sge' @@ -20,4 +18,3 @@ params { // illumina iGenomes reference file paths on GIS Aquila igenomes_base = '/mnt/projects/rpd/genomes.testing/S3_igenomes/' } - diff --git a/conf/hebbe.config b/conf/hebbe.config index 76b8ac7..500ec31 100644 --- a/conf/hebbe.config +++ b/conf/hebbe.config @@ -1,8 +1,7 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'HEBBE' config_profile_description = 'Gothenburg Hebbe cluster profile provided by nf-core/configs.' - config_profile_contact = 'Phil Ewels (@ewels )' + config_profile_contact = 'Phil Ewels (@ewels)' config_profile_url = 'http://www.c3se.chalmers.se/index.php/Hebbe' } diff --git a/conf/mendel.config b/conf/mendel.config index 940a914..aee4ebc 100644 --- a/conf/mendel.config +++ b/conf/mendel.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'MENDEL' config_profile_description = 'GMI MENDEL cluster profile provided by nf-core/configs' config_profile_contact = 'Patrick Hüther (@phue)' config_profile_url = 'http://www.gmi.oeaw.ac.at/' diff --git a/conf/munin.config b/conf/munin.config index a24929e..5d95f01 100644 --- a/conf/munin.config +++ b/conf/munin.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'MUNIN' config_profile_description = 'Big iron cluster profile provided by nf-core/configs.' config_profile_contact = 'Szilveszter Juhos (@szilva)' config_profile_url = '' diff --git a/conf/phoenix.config b/conf/phoenix.config index 685e1e5..b457763 100644 --- a/conf/phoenix.config +++ b/conf/phoenix.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'PHOENIX' config_profile_description = 'University of Adelaide Phoenix HPC cluster profile provided by nf-core/configs' config_profile_contact = 'Yassine Souilmi / Alexander Peltzer (@yassineS, @apeltzer)' config_profile_url = 'https://www.adelaide.edu.au/phoenix/' diff --git a/conf/shh.config b/conf/shh.config index 13b7f5c..4088afd 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'SHH' config_profile_description = 'MPI SHH cluster profile provided by nf-core/configs.' config_profile_contact = 'James Fellows Yates (@jfy133)' config_profile_url = 'https://shh.mpg.de' diff --git a/conf/uct_hex.config b/conf/uct_hex.config index a372000..6e0bbbe 100644 --- a/conf/uct_hex.config +++ b/conf/uct_hex.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'uct_hex' config_profile_description = 'University of Cape Town HEX cluster config file provided by nf-core/configs.' config_profile_contact = 'Katie Lennard (@kviljoen)' config_profile_url = 'http://hpc.uct.ac.za/index.php/hex-3/' @@ -22,4 +21,3 @@ executor{ executor = 'pbs' jobName = { "$task.tag" } } - diff --git a/conf/uppmax-devel.config b/conf/uppmax-devel.config index 760ff77..ad71ac4 100644 --- a/conf/uppmax-devel.config +++ b/conf/uppmax-devel.config @@ -1,6 +1,5 @@ // Profile config names for nf-core/configs params { - config_profile_name = 'UPPMAX-devel' config_profile_description = 'Testing & development profile for UPPMAX, provided by nf-core/configs.' config_profile_contact = 'Phil Ewels (@ewels)' config_profile_url = 'https://www.uppmax.uu.se/' diff --git a/conf/uppmax.config b/conf/uppmax.config index 939b8a7..d2fbc5d 100644 --- a/conf/uppmax.config +++ b/conf/uppmax.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params { - config_profile_name = 'UPPMAX' config_profile_description = 'Swedish UPPMAX cluster profile provided by nf-core/configs.' config_profile_contact = 'Phil Ewels (@ewels)' config_profile_url = 'https://www.uppmax.uu.se/' diff --git a/conf/uzh.config b/conf/uzh.config index 70aad1b..c888096 100644 --- a/conf/uzh.config +++ b/conf/uzh.config @@ -1,6 +1,5 @@ //Profile config names for nf-core/configs params{ - config_profile_name = 'UZH' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' diff --git a/nfcore_custom.config b/nfcore_custom.config index dfcb4d2..f1c9bd4 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -23,9 +23,17 @@ profiles { phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } shh { includeConfig "${params.custom_config_base}/conf/shh.config" } uct_hex { includeConfig "${params.custom_config_base}/conf/uct_hex.config" } - uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config" - includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" - } + uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config" includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" } uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" } uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" } } + +// If user hostnames contain one of these substring and they are +// not running the associated profile, it will trigger a warning message +// Should be defined here for all profiles (not within profile config) +params { + // This is a groovy map, not a nextflow parameter set + hostnames = [ + uppmax: ['.uppmax.uu.se'] + ] +} From d0ca05a22147485c76baeeb897d7201d80c33f0b Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 13 Mar 2019 17:33:23 +0100 Subject: [PATCH 06/38] ; --- nfcore_custom.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nfcore_custom.config b/nfcore_custom.config index f1c9bd4..b21fe62 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -23,7 +23,7 @@ profiles { phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } shh { includeConfig "${params.custom_config_base}/conf/shh.config" } uct_hex { includeConfig "${params.custom_config_base}/conf/uct_hex.config" } - uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config" includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" } + uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" } uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" } uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" } } From 857b0565c239e30c4e1ea45674b618413ae2e541 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 13 Mar 2019 16:51:45 +0000 Subject: [PATCH 07/38] Update nfcore_custom.config --- nfcore_custom.config | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/nfcore_custom.config b/nfcore_custom.config index b21fe62..fbb9984 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -34,6 +34,8 @@ profiles { params { // This is a groovy map, not a nextflow parameter set hostnames = [ - uppmax: ['.uppmax.uu.se'] + uppmax: ['.uppmax.uu.se'], + crick: ['.thecrick.org'] + ] } From 1843b2218c230a9dce4e9d24106b5a363c5611d0 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 13 Mar 2019 16:52:57 +0000 Subject: [PATCH 08/38] Update nfcore_custom.config --- nfcore_custom.config | 1 - 1 file changed, 1 deletion(-) diff --git a/nfcore_custom.config b/nfcore_custom.config index fbb9984..b0c205d 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -36,6 +36,5 @@ params { hostnames = [ uppmax: ['.uppmax.uu.se'], crick: ['.thecrick.org'] - ] } From 26c101a5ab50fa163bc5952fb95b29db90ca16b6 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 13 Mar 2019 16:53:30 +0000 Subject: [PATCH 09/38] Alphabetical order --- nfcore_custom.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nfcore_custom.config b/nfcore_custom.config index b0c205d..61f43a9 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -34,7 +34,7 @@ profiles { params { // This is a groovy map, not a nextflow parameter set hostnames = [ - uppmax: ['.uppmax.uu.se'], - crick: ['.thecrick.org'] + crick: ['.thecrick.org'], + uppmax: ['.uppmax.uu.se'] ] } From 3da1373c147101f16b5bb1306f78d3456ab8c1e3 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 14 Mar 2019 21:16:02 +0100 Subject: [PATCH 10/38] Updated path to centralised singularity cache --- conf/shh.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/shh.config b/conf/shh.config index 4088afd..3b58d23 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -7,7 +7,7 @@ params { singularity { enabled = true - cacheDir = "/projects1/users/$USER/nextflow/nf_cache/singularity/" + cacheDir = "/projects1/singularity_scratch/cache/" } process { From e503a3a0649267d5d3b368ba65d91808987e53f3 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 14 Mar 2019 21:21:31 +0100 Subject: [PATCH 11/38] Added new cluster and singularity cache --- docs/shh.md | 20 ++++++++------------ 1 file changed, 8 insertions(+), 12 deletions(-) diff --git a/docs/shh.md b/docs/shh.md index bcdda3c..67cf3b9 100644 --- a/docs/shh.md +++ b/docs/shh.md @@ -1,21 +1,17 @@ # nf-core/configs: SHH Configuration -All nf-core pipelines have been successfully configured for use on the Department of Archaeogenetic's SDAG cluster at the [Max Planck Institute for the Science of Human History (MPI-SHH)](http://shh.mpg.de). +All nf-core pipelines have been successfully configured for use on the Department of Archaeogenetic's SDAG/CDAG clusters at the [Max Planck Institute for the Science of Human History (MPI-SHH)](http://shh.mpg.de). -To use, run the pipeline with `-profile shh`. This will download and launch the [`shh.config`](../conf/shh.config) which has been pre-configured with a setup suitable for the SDAG cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. - -Note that the configuration file is currently optimised for `nf-core/eager`. It -will submit to the medium queue but with a walltime of 48 hours. - -## Preparation -Before running the pipeline you will need to create a the following folder in your `/projects1/users/` directory. This will be used to store the singularity software images, which will take up too much space for your home directory. - -This should be named as follows, replacing `` with your username: +To use, run the pipeline with `-profile shh`. This will download and launch the [`shh.config`](../conf/shh.config) which has been pre-configured with a setup suitable for the SDAG and CDAG clusters. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. The image will currently be centrally stored here: ```bash -"/projects1/users//nextflow/nf_cache/singularity/" +/projects1/singularity_scratch/cache/ ``` +however this will likely change to a read-only directory in the future that will be managed by IT. + +Note that **the configuration file is currently optimised for `nf-core/eager`**. It will submit to the short queue but with a walltime of 2 hours. + >NB: You will need an account and VPN access to use the cluster at MPI-SHH in order to run the pipeline. If in doubt contact IT. ->NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the lhead nodes. If in doubt contact IT. +>NB: Nextflow will need to submit the jobs via SLURM to the clusters and as such the commands above will have to be executed on one of the head nodes. If in doubt contact IT. From ecb36dd8c23ab72d1f507237eba0740efe02f136 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 14 Mar 2019 21:26:43 +0100 Subject: [PATCH 12/38] Reduced memory and CPUs for cdag compatibility Also matches 'fair use' policy --- conf/shh.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/shh.config b/conf/shh.config index 3b58d23..43d192f 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -16,7 +16,7 @@ process { } params { - max_memory = 734.GB - max_cpus = 64 + max_memory = 256.GB + max_cpus = 32 max_time = 2.h } From 0929349303821693e66c3fc9f9929b4a6bbc00c9 Mon Sep 17 00:00:00 2001 From: maxibor Date: Mon, 18 Mar 2019 11:13:11 +0100 Subject: [PATCH 13/38] add queueSize limited to 5 --- conf/shh.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/shh.config b/conf/shh.config index 43d192f..92db897 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -13,6 +13,7 @@ singularity { process { executor = 'slurm' queue = 'short' + queueSize = 5 } params { From 76a5fcf0776e3391aeeda4d3e9d1a9f193e1dde7 Mon Sep 17 00:00:00 2001 From: maxibor Date: Wed, 20 Mar 2019 13:44:13 +0100 Subject: [PATCH 14/38] switch to queueSize 16 for shh config --- conf/shh.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/shh.config b/conf/shh.config index 92db897..159de89 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -13,7 +13,7 @@ singularity { process { executor = 'slurm' queue = 'short' - queueSize = 5 + queueSize = 16 } params { From 51c2a54399e0a743eccd38ca2536674e7ee979f2 Mon Sep 17 00:00:00 2001 From: Tobias Schraink Date: Wed, 17 Apr 2019 16:59:38 -0400 Subject: [PATCH 15/38] added nyu prince and bigpurple configs --- conf/bigpurple.config | 23 +++++++++++++++++++++++ conf/prince.config | 21 +++++++++++++++++++++ nfcore_custom.config | 2 ++ 3 files changed, 46 insertions(+) create mode 100644 conf/bigpurple.config create mode 100644 conf/prince.config diff --git a/conf/bigpurple.config b/conf/bigpurple.config new file mode 100644 index 0000000..b7850db --- /dev/null +++ b/conf/bigpurple.config @@ -0,0 +1,23 @@ +params { + config_profile_description = """ + NYU School of Medicine BigPurple cluster profile provided by nf-core/configs. + module load both singularity/3.1 and squashfs-tools/4.3 before running the pipeline with this profile! + Also consider running the pipeline on a compute node the first time, as it will be pulling the docker image, which will be converted into a singularity image, which is heavy on the login node. Subsequent runs can be done on the login node, as the docker image will only be pulled and converted once. By default the images will be stored in ./work/singularity + """.stripIndents() + config_profile_contact = 'Tobias Schraink (@tobsecret)' + config_profile_url = 'https://genome.med.nyu.edu/hpcf/wiki/Manual:Cluster_User_Guide' +} + +singularity { + enabled = true + autoMounts = true +} + +process { + beforeScript = """ + module load singularity/3.1 + module load squashfs-tools/4.3 + """ + .stripIndent() + executor = 'slurm' +} diff --git a/conf/prince.config b/conf/prince.config new file mode 100644 index 0000000..5fc07c6 --- /dev/null +++ b/conf/prince.config @@ -0,0 +1,21 @@ +params { + config_profile_description = """ + NYU prince cluster profile provided by nf-core/configs. + Please consider running the pipeline on a compute node the first time, as it will be pulling the docker image, which will be converted into a singularity image, which is heavy on the login node. Subsequent runs can be done on the login node, as the docker image will only be pulled and converted once. By default the images will be stored in ./work/singularity + """.stripIndent() + config_profile_contact = 'Tobias Schraink (@tobsecret)' + config_profile_url = 'https://wikis.nyu.edu/display/NYUHPC/Clusters+-+Prince' +} + +singularity { + enabled = true +} + +process { + beforeScript = """ + module load singularity/3.1.0 + module load squashfs/4.3 + """ + .stripIndent() + executor = 'slurm' +} diff --git a/nfcore_custom.config b/nfcore_custom.config index 61f43a9..7374fa0 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -26,6 +26,8 @@ profiles { uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" } uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" } uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" } + prince { includeConfig "${params.custom_config_base}/conf/prince.config" } + bigpurple { includeConfig "${params.custom_config_base}/conf/bigpurple.config" } } // If user hostnames contain one of these substring and they are From 4a915e330a7e0bb8e02c4e5d7739f4364b21ae32 Mon Sep 17 00:00:00 2001 From: Tobias Schraink Date: Wed, 17 Apr 2019 17:15:16 -0400 Subject: [PATCH 16/38] added warnings to run on SCRATCH --- conf/bigpurple.config | 3 ++- conf/prince.config | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/conf/bigpurple.config b/conf/bigpurple.config index b7850db..967cc5f 100644 --- a/conf/bigpurple.config +++ b/conf/bigpurple.config @@ -1,7 +1,8 @@ params { config_profile_description = """ NYU School of Medicine BigPurple cluster profile provided by nf-core/configs. - module load both singularity/3.1 and squashfs-tools/4.3 before running the pipeline with this profile! + module load both singularity/3.1 and squashfs-tools/4.3 before running the pipeline with this profile!! + Run from your scratch or lab directory - Nextflow makes a lot of files!! Also consider running the pipeline on a compute node the first time, as it will be pulling the docker image, which will be converted into a singularity image, which is heavy on the login node. Subsequent runs can be done on the login node, as the docker image will only be pulled and converted once. By default the images will be stored in ./work/singularity """.stripIndents() config_profile_contact = 'Tobias Schraink (@tobsecret)' diff --git a/conf/prince.config b/conf/prince.config index 5fc07c6..76b32ed 100644 --- a/conf/prince.config +++ b/conf/prince.config @@ -1,6 +1,7 @@ params { config_profile_description = """ NYU prince cluster profile provided by nf-core/configs. + Run from your scratch directory, the output files may be large! Please consider running the pipeline on a compute node the first time, as it will be pulling the docker image, which will be converted into a singularity image, which is heavy on the login node. Subsequent runs can be done on the login node, as the docker image will only be pulled and converted once. By default the images will be stored in ./work/singularity """.stripIndent() config_profile_contact = 'Tobias Schraink (@tobsecret)' From 1772f4119c391a4df4d6f7d4219b537d375485ec Mon Sep 17 00:00:00 2001 From: maxibor Date: Thu, 18 Apr 2019 11:19:53 +0200 Subject: [PATCH 17/38] adding igenomes to shh config --- conf/shh.config | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/conf/shh.config b/conf/shh.config index 159de89..020be37 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -2,7 +2,7 @@ params { config_profile_description = 'MPI SHH cluster profile provided by nf-core/configs.' config_profile_contact = 'James Fellows Yates (@jfy133)' - config_profile_url = 'https://shh.mpg.de' + config_profile_url = 'https: //shh.mpg.de' } singularity { @@ -20,4 +20,6 @@ params { max_memory = 256.GB max_cpus = 32 max_time = 2.h -} + //Illumina iGenomes reference file path + igenomes_base = "/projects1/public_data/igenomes/" +} \ No newline at end of file From 9d9ac4c3bb33f41561c402b122c36fbed8771e28 Mon Sep 17 00:00:00 2001 From: maxibor Date: Thu, 18 Apr 2019 11:22:54 +0200 Subject: [PATCH 18/38] remove whitespace --- conf/shh.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/shh.config b/conf/shh.config index 020be37..d2feaff 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -2,7 +2,7 @@ params { config_profile_description = 'MPI SHH cluster profile provided by nf-core/configs.' config_profile_contact = 'James Fellows Yates (@jfy133)' - config_profile_url = 'https: //shh.mpg.de' + config_profile_url = 'https://shh.mpg.de' } singularity { From 4ba831705dc9bf0fb14764ffedf99f97cc1e9c75 Mon Sep 17 00:00:00 2001 From: Tobias Schraink Date: Thu, 18 Apr 2019 14:13:02 -0400 Subject: [PATCH 19/38] added nyu prince and bigpurple md files, added singularity cacheDir to prince and bigpurple configs --- conf/bigpurple.config | 9 ++++++--- conf/prince.config | 7 +++++-- docs/bigpurple.md | 23 +++++++++++++++++++++++ docs/prince.md | 19 +++++++++++++++++++ 4 files changed, 53 insertions(+), 5 deletions(-) create mode 100644 docs/bigpurple.md create mode 100644 docs/prince.md diff --git a/conf/bigpurple.config b/conf/bigpurple.config index 967cc5f..5fdf7e8 100644 --- a/conf/bigpurple.config +++ b/conf/bigpurple.config @@ -1,17 +1,20 @@ +singularityDir = "/gpfs/scratch/${USER}/singularity_images_nextflow" + params { config_profile_description = """ NYU School of Medicine BigPurple cluster profile provided by nf-core/configs. module load both singularity/3.1 and squashfs-tools/4.3 before running the pipeline with this profile!! Run from your scratch or lab directory - Nextflow makes a lot of files!! - Also consider running the pipeline on a compute node the first time, as it will be pulling the docker image, which will be converted into a singularity image, which is heavy on the login node. Subsequent runs can be done on the login node, as the docker image will only be pulled and converted once. By default the images will be stored in ./work/singularity - """.stripIndents() + Also consider running the pipeline on a compute node (srun --pty /bin/bash -t=01:00:00) the first time, as it will be pulling the docker image, which will be converted into a singularity image, which is heavy on the login node and will take some time. Subsequent runs can be done on the login node, as the docker image will only be pulled and converted once. By default the images will be stored in $singularityDir + """.stripIndent() config_profile_contact = 'Tobias Schraink (@tobsecret)' - config_profile_url = 'https://genome.med.nyu.edu/hpcf/wiki/Manual:Cluster_User_Guide' + config_profile_url = 'https://github.com/nf-core/configs/blob/master/docs/bigpurple.md' } singularity { enabled = true autoMounts = true + cacheDir = singularityDir } process { diff --git a/conf/prince.config b/conf/prince.config index 76b32ed..6ae4ee8 100644 --- a/conf/prince.config +++ b/conf/prince.config @@ -1,15 +1,18 @@ +singularityDir = "$SCRATCH/singularity_images_nextflow" + params { config_profile_description = """ NYU prince cluster profile provided by nf-core/configs. Run from your scratch directory, the output files may be large! - Please consider running the pipeline on a compute node the first time, as it will be pulling the docker image, which will be converted into a singularity image, which is heavy on the login node. Subsequent runs can be done on the login node, as the docker image will only be pulled and converted once. By default the images will be stored in ./work/singularity + Please consider running the pipeline on a compute node the first time, as it will be pulling the docker image, which will be converted into a singularity image, which is heavy on the login node. Subsequent runs can be done on the login node, as the docker image will only be pulled and converted once. By default the images will be stored in $singularityDir """.stripIndent() config_profile_contact = 'Tobias Schraink (@tobsecret)' - config_profile_url = 'https://wikis.nyu.edu/display/NYUHPC/Clusters+-+Prince' + config_profile_url = 'https://github.com/nf-core/configs/blob/master/docs/prince.md' } singularity { enabled = true + cacheDir = singularityDir } process { diff --git a/docs/bigpurple.md b/docs/bigpurple.md new file mode 100644 index 0000000..e3b8dfb --- /dev/null +++ b/docs/bigpurple.md @@ -0,0 +1,23 @@ +# nf-core/configs: BigPurple Configuration +## nf-core pipelines that use this repo +All nf-core pipelines that use this config repo (which is most), can be run on BigPurple. **Before** running a pipeline for the first time, go into an interactive slurm session on a compute node (`srun --pty --time=02:00:00 -c 2`), as the docker image for the pipeline will need to be pulled and converted. Once in the interactive session: + +``` +module load singularity/3.1 +module load squashfs-tools/4.3 +``` + +Now, run the pipeline of your choice with `-profile bigpurple`. This will download and launch the bigpurple.config which has been pre-configured with a setup suitable for the BigPurple cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a singularity image before execution of the pipeline. +An example commandline: + +`nextflow run nf-core/ -profile bigpurple ` + +## nf-core pipelines that do not use this repo +If the pipeline has not yet been configured to use this config, then you will have to do it manually. +git clone this repo, copy the `bigpurple.config` from the conf folder and then you can invoke the pipeline like this: + +`nextflow run nf-core/ -c bigpurple.config ` + + +>NB: You will need an account to use the HPC cluster BigPurple in order to run the pipeline. If in doubt contact MCIT. +>NB: You will need to install nextflow in your home directory - instructions are on nextflow.io (or ask the writer of this profile). The reason there is no module for nextflow on the cluster, is that the development cycle of nextflow is rapid and it's easy to update yourself: `nextflow self-update` diff --git a/docs/prince.md b/docs/prince.md new file mode 100644 index 0000000..9a49ee0 --- /dev/null +++ b/docs/prince.md @@ -0,0 +1,19 @@ +# nf-core/configs: Prince Configuration +## nf-core pipelines that use this repo +All nf-core pipelines that use this config repo (which is most), can be run on prince. **Before** running a pipeline for the first time, go into an interactive slurm session on a compute node (`srun --pty --time=02:00:00 -c 2`), as the docker image for the pipeline will need to be pulled and converted. + +Now, run the pipeline of your choice with `-profile prince`. This will download and launch the prince.config which has been pre-configured with a setup suitable for the prince cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a singularity image before execution of the pipeline. This step **takes time**!! +An example commandline: + +`nextflow run nf-core/ -profile prince ` + +## nf-core pipelines that do not use this repo +If the pipeline has not yet been configured to use this config, then you will have to do it manually. +git clone this repo, copy the `prince.config` from the conf folder and then you can invoke the pipeline like this: + +`nextflow run nf-core/ -c prince.config ` + + +>NB: You will need an account to use the HPC cluster Prince in order to run the pipeline. If in doubt contact the HPC admins. +>NB: Rather than using the nextflow module, I recommend you install nextflow in your home directory - instructions are on nextflow.io (or ask the writer of this profile). The reason this is better than using the module for nextflow on the cluster, is that the development cycle of nextflow is rapid and it's easy to update your installation yourself: `nextflow self-update` + From b6c1d3ba518ce5c046f698bddd644973448381df Mon Sep 17 00:00:00 2001 From: Tobias Schraink Date: Thu, 18 Apr 2019 14:23:17 -0400 Subject: [PATCH 20/38] added bigpurple and prince doc links in README --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index acb2ea4..eadd3bb 100644 --- a/README.md +++ b/README.md @@ -85,6 +85,7 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs Currently documentation is available for the following clusters: * [BINAC](docs/binac.md) +* [BIGPURPLE](docs/bigpurple.md) * [CCGA](docs/ccga.md) * [CFC](docs/binac.md) * [CRICK](docs/crick.md) @@ -93,6 +94,7 @@ Currently documentation is available for the following clusters: * [MENDEL](docs/mendel.md) * [MUNIN](docs/munin.md) * [PHOENIX](docs/phoenix.md) +* [PRINCE](docs/prince.md) * [SHH](docs/shh.md) * [UCT_HEX](docs/uct_hex.md) * [UPPMAX-DEVEL](docs/uppmax-devel.md) From d91b06d884dfbb86f537662460f07e9f2859dbd6 Mon Sep 17 00:00:00 2001 From: Tobias Schraink Date: Thu, 18 Apr 2019 14:25:27 -0400 Subject: [PATCH 21/38] added missing line in prince and bigpurple docs --- docs/bigpurple.md | 1 + docs/prince.md | 1 + 2 files changed, 2 insertions(+) diff --git a/docs/bigpurple.md b/docs/bigpurple.md index e3b8dfb..19b0352 100644 --- a/docs/bigpurple.md +++ b/docs/bigpurple.md @@ -20,4 +20,5 @@ git clone this repo, copy the `bigpurple.config` from the conf folder and then y >NB: You will need an account to use the HPC cluster BigPurple in order to run the pipeline. If in doubt contact MCIT. + >NB: You will need to install nextflow in your home directory - instructions are on nextflow.io (or ask the writer of this profile). The reason there is no module for nextflow on the cluster, is that the development cycle of nextflow is rapid and it's easy to update yourself: `nextflow self-update` diff --git a/docs/prince.md b/docs/prince.md index 9a49ee0..12f5e65 100644 --- a/docs/prince.md +++ b/docs/prince.md @@ -15,5 +15,6 @@ git clone this repo, copy the `prince.config` from the conf folder and then you >NB: You will need an account to use the HPC cluster Prince in order to run the pipeline. If in doubt contact the HPC admins. + >NB: Rather than using the nextflow module, I recommend you install nextflow in your home directory - instructions are on nextflow.io (or ask the writer of this profile). The reason this is better than using the module for nextflow on the cluster, is that the development cycle of nextflow is rapid and it's easy to update your installation yourself: `nextflow self-update` From efd831a8a34fe7cae2225faf71eaa72383c13edb Mon Sep 17 00:00:00 2001 From: maxibor Date: Thu, 25 Apr 2019 15:48:20 +0200 Subject: [PATCH 22/38] add automounts for singularity --- conf/shh.config | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/conf/shh.config b/conf/shh.config index d2feaff..fd16e9e 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -2,11 +2,12 @@ params { config_profile_description = 'MPI SHH cluster profile provided by nf-core/configs.' config_profile_contact = 'James Fellows Yates (@jfy133)' - config_profile_url = 'https://shh.mpg.de' + config_profile_url = 'https: //shh.mpg.de' } singularity { enabled = true + autoMounts = true cacheDir = "/projects1/singularity_scratch/cache/" } From de1b2aa7d27bff386595f802bab47939690ef022 Mon Sep 17 00:00:00 2001 From: maxibor Date: Thu, 25 Apr 2019 15:50:48 +0200 Subject: [PATCH 23/38] remove autoformat added space --- conf/shh.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/shh.config b/conf/shh.config index fd16e9e..2b195a6 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -2,7 +2,7 @@ params { config_profile_description = 'MPI SHH cluster profile provided by nf-core/configs.' config_profile_contact = 'James Fellows Yates (@jfy133)' - config_profile_url = 'https: //shh.mpg.de' + config_profile_url = 'https://shh.mpg.de' } singularity { From 441ddbcdab01871842451bf4b33d757d8c63d87a Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 28 May 2019 15:25:10 +0200 Subject: [PATCH 24/38] Newest Update is 3.0.3 --- conf/binac.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/binac.config b/conf/binac.config index 5df94bf..0e69d4a 100644 --- a/conf/binac.config +++ b/conf/binac.config @@ -10,7 +10,7 @@ singularity { } process { - beforeScript = 'module load devel/singularity/3.0.1' + beforeScript = 'module load devel/singularity/3.0.3' executor = 'pbs' queue = 'short' } From 66eeeebe81d1aef1d8083e492484e47975d8760b Mon Sep 17 00:00:00 2001 From: Olga Botvinnik Date: Thu, 30 May 2019 11:15:38 -0700 Subject: [PATCH 25/38] Initial commit of CZBiohub --- conf/czbiohub.config | 98 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 98 insertions(+) create mode 100644 conf/czbiohub.config diff --git a/conf/czbiohub.config b/conf/czbiohub.config new file mode 100644 index 0000000..ff1523e --- /dev/null +++ b/conf/czbiohub.config @@ -0,0 +1,98 @@ +/* + * ------------------------------------------------- + * Nextflow config file for UPPMAX (milou / irma) + * ------------------------------------------------- + * Defines reference genomes, using iGenome paths + * Imported under the default 'standard' Nextflow + * profile in nextflow.config + */ + +docker { + enabled = true +} + +process { + executor = 'awsbatch' +} + +params { + saveReference = true + + // Largest SPOT instances available on AWS: https://ec2instances.info/ + max_memory = 1952.GB + max_cpus = 96 + max_time = 240.h + + // illumina iGenomes reference file paths on CZ Biohub reference s3 bucket + // No final slash because it's added later + igenomes_base = "s3://czbiohub-reference/igenomes" + + // GENCODE (human + mouse) reference file paths on CZ Biohub reference s3 bucket + // No final slash because it's added later + gencode_base = "s3://czbiohub-reference/gencode" + transgenes_base = "s3://czbiohub-reference/transgenes" + + // AWS configurations + awsregion = "us-west-2" + awsqueue = "nextflow" + workDir = "s3://czb-nextflow/rnaseq/" + + // GENCODE GTF and fasta files + genomes { + 'GRCh38' { + fasta = "${params.gencode_base}/human/v29/GRCh38.p12.genome.fa.gz" + gtf = "${params.gencode_base}/human/v29/gencode.vM19.annotation.gtf.gz" + } + 'GRCm38' { + fasta = "${params.gencode_base}/mouse/vM19/GRCm38.p6.genome.fa.gz" + gtf = "${params.gencode_base}/mouse/vM19/gencode.vM19.annotation.gtf.gz" + } + } + + transgenes { + 'ChR2' { + fasta = "${params.transgenes_base}/ChR2/ChR2.fa.gz" + gtf = "${params.transgenes_base}/ChR2/ChR2.gtf.gz" + } + 'Cre' { + fasta = "${params.transgenes_base}/Cre/Cre.fa.gz" + gtf = "${params.transgenes_base}/Cre/Cre.gtf.gz" + } + 'ERCC' { + fasta = "${params.transgenes_base}/ERCC92/ERCC92.fa.gz" + gtf = "${params.transgenes_base}/ERCC92/ERCC92.gtf.gz" + } + 'GCaMP6m' { + fasta = "${params.transgenes_base}/GCaMP6m/GCaMP6m.fa.gz" + gtf = "${params.transgenes_base}/GCaMP6m/GCaMP6m.gtf.gz" + } + 'GFP' { + fasta = "${params.transgenes_base}/Gfp/Gfp.fa.gz" + gtf = "${params.transgenes_base}/Gfp/Gfp.gtf.gz" + } + 'NpHR' { + fasta = "${params.transgenes_base}/NpHR/NpHR.fa.gz" + gtf = "${params.transgenes_base}/NpHR/NpHR.gtf.gz" + } + 'RCaMP' { + fasta = "${params.transgenes_base}/RCaMP/RCaMP.fa.gz" + gtf = "${params.transgenes_base}/RCaMP/RCaMP.gtf.gz" + } + 'RGECO' { + fasta = "${params.transgenes_base}/RGECO/RGECO.fa.gz" + gtf = "${params.transgenes_base}/RGECO/RGECO.gtf.gz" + } + 'Tdtom' { + fasta = "${params.transgenes_base}/Tdtom/Tdtom.fa.gz" + gtf = "${params.transgenes_base}/Tdtom/Tdtom.gtf.gz" + } + 'Car-T' { + fasta = "${params.transgenes_base}/car-t/car-t.fa.gz" + gtf = "${params.transgenes_base}/car-t/car-t.gtf.gz" + } + 'zsGreen' { + fasta = "${params.transgenes_base}/zsGreen/zsGreen.fa.gz" + gtf = "${params.transgenes_base}/zsGreen/zsGreen.gtf.gz" + } + } +} From ac804859f42a2bfa20a7f9c6fbbc27915729ed47 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 31 May 2019 00:47:06 +0100 Subject: [PATCH 26/38] Add nf-core logo --- README.md | 4 +--- docs/images/nfcore-configs_logo.png | Bin 0 -> 14072 bytes 2 files changed, 1 insertion(+), 3 deletions(-) create mode 100755 docs/images/nfcore-configs_logo.png diff --git a/README.md b/README.md index 6a53642..75d6199 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,4 @@ - - -# [nf-core/configs](https://github.com/nf-core/configs) +# ![nf-core/configs](docs/images/nfcore-configs_logo.png) [![Build Status](https://travis-ci.org/nf-core/configs.svg?branch=master)](https://travis-ci.org/nf-core/configs) diff --git a/docs/images/nfcore-configs_logo.png b/docs/images/nfcore-configs_logo.png new file mode 100755 index 0000000000000000000000000000000000000000..eef073868983145737377f81cb92f40132f3c866 GIT binary patch literal 14072 zcmaKTWmp_d(>3ny?gY2s9(?ft2`(Gl-QC@mU_leIgy8PBIKeHrySwYVxu5U%x7Vys zb$9htcTJyjI_9IA0wx+68Vn2!rXoOA69xu$3i^2v1qu3Us1FQ+z9G0tD}F+OKKxP4 zqoLnXodJ4oFfd3}|DLdJf}0!AA4%QibltU_EZx1nxLUw?d3kZ#ING_HeQ~znbaJ)I zJ{2Q_fuVs>l$HAAopX}wv^Ebr+^Rq}@wV^zLb^ES_C?aY3|Jw06oT z--@bqr2Vd}UUVFlVkb-H4%8+Vk6r;$v?0k`6_HV$CFoG zgFsFrWq6~;-vI1U2nC~pg2?_QPKq#k?+Rzt`OFtxHzv#`B{)Rd^N*%Wc{lU4xY^sMclgQ7~(ocU~sUpEhzIz_|mh^Ri zwT||GjZd-MuKGgB{>lzyg4yCdT=>RI%{hDTD_;Wb%T$4WW9iu#IIY+NS*f3%P+yfm 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OB}#(hK&ZWj3s`n{7HrqjtxUSa`@>~z?#eOju(Nt1z7pe-=|v*U=Ekv- zvB>rJh)W)ALCqQR(daQ*!uj&;)>8ua32{)Bh?V|;Di~W#_Yw|bx5d{m*`?_=2jD2t z`SJ?v`+8pBDQ?^7(F}h|ql35_SF4RIz}n1;bo;S<2~S||*ug7PS2x`L^I#c}?Z>#} zkSMmzuWX2<9sEv{}ruJgU^VCR&2SE z;p;lUs6OB)Gwv+O-1kV$020>bKYQ^r5v(bd@qa0TKFB_9WdibISQ%MxH#Y+NH_0lf z87r3bDWM+hLjz<&dPC{bB^Sq+V7J|n{q%zpNx#PP3mNbO#ujUNGIyeTC$xjji_Kao zqXX@VI?Y5sW7@VO1SCZ)q@ieOFrv1FM|T@ax$wfWqUvmY(rDP+c%|_wcc*3?2C;HJ zOvUW$%=Az$rRhJ0;)x$Qa|P`_b|~ZVLn@PVZg~Ja@zUt~@Hrt+RVeN{?3qY|c<}wW zVgQ5s2%?T+!!Ks^$+d2jlaDEK6NEM#RoyP}0TfG&AXR|NWlwV3;&iY9%kr#~*QZ*Y z7#M8tfocarx&cDLiYb4S_=!la4Jsc!r6E40jeF>DpatoJD74|Vf-C92&g4SL=ci}^ zuLgcq+0@K)lslTv@O%6mBPO^adFvk1#1m~ebhsIL>X=p$J(dg9lm=I< z3G$e>0KU*b{&fIqLX@>h3)STrmLXNHuv(L?*Qp}kp7IKagPGVk2IybtvF_WOf;5&m zm5c|(KZkLKb0*j*!S4$YE3AVP+xCB_0y;VZ@g_)fBYbmd?Co^Mo@tt`Hj;V8zQf+y z!i}$F$ne(&S4NRQbB=QKZJ%k-@==ArfMkeMgtbX@j%#6pM*fI6zbrK�+w#YfYu9x==Sog@SmS=U`POT9?AfMG-ESqPBdf{8;3K+yCxUZ< zbK8c_uOYeCk0Dc3F7j(q+P!hfz)&tw=kbDx%ebgrlnO%y)4YJXsQK+1#i^}44Pzcb zA?;m+wO#NMh*^iY8Wg}%(bPi~y?d$^p7j0AHM)UUCb67(X#xuuxeBpGn|9}`guLaN z)Y1#z_m`kJNIxM&93Z>i1*!NTx&FcY$d|4rjlwf0>5rt*F4;i!Yx4yaGNK-qaA?)8mN| zME*?9{c)GPk{$sul_jd=)!g>wlHILk-PYBpMs~)hvwRaNaJ;5Ae}9X+G%M+deHChJo#HOHA3&mN7)~BBMP~Ceh%QKfprNg;N z$fpAGSW-ANT#=nwHZF$?x)mCRgGd``l_pWOt~?0~4ha<|k7h^w03S{9yvkGY7I*=c&@fz&@Sl@2aZQ_LRhM?C9@@)TwUKZQ%hq|y}Ac|fp1 zt}^PxvpFZ3Nz5?K?=g!7??3VFZudzh6NGVJS}57zTgvH=Yi?)mkfCL~w+LCI$#0ad zp+Ie76R?A7GpdQ_S}J4lSO)0S=w$ADFLo<3f-7+xVj8w^^=hOS41?NL9Df85e@dq9 zWJ3+b(8w4h58w7tcv#3rr^r2dlNpc*MSC9%zKNH4HyH8CULhA68(TaNu9Gqh|4BV= z44?cdaVr=%9AEmk3|ygV zXtj=LVmo(e^&7govvs3HX!Vg^$kI`gFS?7s`!0&u?W{c5%0Gs+~&!W@mLl~#>Tj)JHXIc*8H8umI0xMOeP_%FT>jOWN|Evn*g z<2d_^wxq$(cFZ=prmRp-a5At&1}Aq?9JjeTk%M1)DojHDI1v6DOq=|Bxa`yhIW$~O z5>$%tPpV`erbUJAK%dv$2EQGZ4wjVD#(@eJ9yCMzcCvh1=qk-jwn=QLU561ZaY*|~ z0jEzG;C;F3d`2bmA`;$@$=@uEK>cXSOy;H&A>(YV=E=yDO6DHFm=y~#zV+V9O02Qf z%=J^8U~FPs84=EI7{js<+iYLWBQD_G-up{;V7;(Ix3Vy!nhH7YB_EEY3aDqgsmf{S zV^_es=F8hg`~y}}X;@@irYz(h0T{QeN(B>y#RUvsX(2oWd%V6jo?^tSF;h6utvqru zv0EU*HUD)5KnZ|W2oLqW>*!yx>JOeQ&;yFLA9cY1FOne;+~${@{dWu{ z+W$5k;VEb()@^(ai~hWf=#M_RJ<7;Eg+Dp=N=QeCr!8#lO2G9=Ln)UzRhB@GMZzLF z{mM8Yume%!lYY{6;xAkf=oG+dnYxVY5)`YM0writXXOy9pm!ra_#6@y%)#;}tg$JQ zH~gOD${4Il*|Pt@s0UZJb7|=4Qquf~F)2y3q4*0r(i1Q$Ld^*nnVsnCZO}gh4K-f94z;@N@KPpW@8fpw2P&OokJyp!l_89P8{8|3j>pBR09$ zrGUJBZg~>te9jb_#|Ho0RLZLWB#)or>On9jMaIb($nK&(ylu8I$k~YR$7^XQC2>Ny zfiRo*NamGl(HKCHCnw)Fo*yE literal 0 HcmV?d00001 From 1b2fcf5a98f36dc74a236b589ad79e0dcd109587 Mon Sep 17 00:00:00 2001 From: Olga Botvinnik Date: Fri, 31 May 2019 08:16:51 -0700 Subject: [PATCH 27/38] Add author lines --- conf/czbiohub.config | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/conf/czbiohub.config b/conf/czbiohub.config index ff1523e..1c788b9 100644 --- a/conf/czbiohub.config +++ b/conf/czbiohub.config @@ -1,12 +1,19 @@ /* * ------------------------------------------------- - * Nextflow config file for UPPMAX (milou / irma) + * Nextflow config file for Chan Zuckerberg Biohub * ------------------------------------------------- * Defines reference genomes, using iGenome paths * Imported under the default 'standard' Nextflow * profile in nextflow.config */ + //Profile config names for nf-core/configs + params { + config_profile_description = 'Chan Zuckerberg Biohub AWS Batch profile provided by nf-core/configs.' + config_profile_contact = 'Olga Botvinnik (@olgabot)' + config_profile_url = 'https://www.czbiohub.org/' + } + docker { enabled = true } From 9c0315addb194e2360c6fe76d53a9947d3866fab Mon Sep 17 00:00:00 2001 From: Olga Botvinnik Date: Fri, 31 May 2019 13:17:48 -0700 Subject: [PATCH 28/38] Use flat nongzipped files --- conf/czbiohub.config | 52 ++++++++++++++++++++++---------------------- 1 file changed, 26 insertions(+), 26 deletions(-) diff --git a/conf/czbiohub.config b/conf/czbiohub.config index 1c788b9..d51c6f2 100644 --- a/conf/czbiohub.config +++ b/conf/czbiohub.config @@ -47,59 +47,59 @@ params { // GENCODE GTF and fasta files genomes { 'GRCh38' { - fasta = "${params.gencode_base}/human/v29/GRCh38.p12.genome.fa.gz" - gtf = "${params.gencode_base}/human/v29/gencode.vM19.annotation.gtf.gz" + fasta = "${params.gencode_base}/human/v29/GRCh38.p12.genome.fa" + gtf = "${params.gencode_base}/human/v29/gencode.vM19.annotation.gtf" } 'GRCm38' { - fasta = "${params.gencode_base}/mouse/vM19/GRCm38.p6.genome.fa.gz" - gtf = "${params.gencode_base}/mouse/vM19/gencode.vM19.annotation.gtf.gz" + fasta = "${params.gencode_base}/mouse/vM19/GRCm38.p6.genome.fa" + gtf = "${params.gencode_base}/mouse/vM19/gencode.vM19.annotation.gtf" } } transgenes { 'ChR2' { - fasta = "${params.transgenes_base}/ChR2/ChR2.fa.gz" - gtf = "${params.transgenes_base}/ChR2/ChR2.gtf.gz" + fasta = "${params.transgenes_base}/ChR2/ChR2.fa" + gtf = "${params.transgenes_base}/ChR2/ChR2.gtf" } 'Cre' { - fasta = "${params.transgenes_base}/Cre/Cre.fa.gz" - gtf = "${params.transgenes_base}/Cre/Cre.gtf.gz" + fasta = "${params.transgenes_base}/Cre/Cre.fa" + gtf = "${params.transgenes_base}/Cre/Cre.gtf" } 'ERCC' { - fasta = "${params.transgenes_base}/ERCC92/ERCC92.fa.gz" - gtf = "${params.transgenes_base}/ERCC92/ERCC92.gtf.gz" + fasta = "${params.transgenes_base}/ERCC92/ERCC92.fa" + gtf = "${params.transgenes_base}/ERCC92/ERCC92.gtf" } 'GCaMP6m' { - fasta = "${params.transgenes_base}/GCaMP6m/GCaMP6m.fa.gz" - gtf = "${params.transgenes_base}/GCaMP6m/GCaMP6m.gtf.gz" + fasta = "${params.transgenes_base}/GCaMP6m/GCaMP6m.fa" + gtf = "${params.transgenes_base}/GCaMP6m/GCaMP6m.gtf" } 'GFP' { - fasta = "${params.transgenes_base}/Gfp/Gfp.fa.gz" - gtf = "${params.transgenes_base}/Gfp/Gfp.gtf.gz" + fasta = "${params.transgenes_base}/Gfp/Gfp.fa" + gtf = "${params.transgenes_base}/Gfp/Gfp.gtf" } 'NpHR' { - fasta = "${params.transgenes_base}/NpHR/NpHR.fa.gz" - gtf = "${params.transgenes_base}/NpHR/NpHR.gtf.gz" + fasta = "${params.transgenes_base}/NpHR/NpHR.fa" + gtf = "${params.transgenes_base}/NpHR/NpHR.gtf" } 'RCaMP' { - fasta = "${params.transgenes_base}/RCaMP/RCaMP.fa.gz" - gtf = "${params.transgenes_base}/RCaMP/RCaMP.gtf.gz" + fasta = "${params.transgenes_base}/RCaMP/RCaMP.fa" + gtf = "${params.transgenes_base}/RCaMP/RCaMP.gtf" } 'RGECO' { - fasta = "${params.transgenes_base}/RGECO/RGECO.fa.gz" - gtf = "${params.transgenes_base}/RGECO/RGECO.gtf.gz" + fasta = "${params.transgenes_base}/RGECO/RGECO.fa" + gtf = "${params.transgenes_base}/RGECO/RGECO.gtf" } 'Tdtom' { - fasta = "${params.transgenes_base}/Tdtom/Tdtom.fa.gz" - gtf = "${params.transgenes_base}/Tdtom/Tdtom.gtf.gz" + fasta = "${params.transgenes_base}/Tdtom/Tdtom.fa" + gtf = "${params.transgenes_base}/Tdtom/Tdtom.gtf" } 'Car-T' { - fasta = "${params.transgenes_base}/car-t/car-t.fa.gz" - gtf = "${params.transgenes_base}/car-t/car-t.gtf.gz" + fasta = "${params.transgenes_base}/car-t/car-t.fa" + gtf = "${params.transgenes_base}/car-t/car-t.gtf" } 'zsGreen' { - fasta = "${params.transgenes_base}/zsGreen/zsGreen.fa.gz" - gtf = "${params.transgenes_base}/zsGreen/zsGreen.gtf.gz" + fasta = "${params.transgenes_base}/zsGreen/zsGreen.fa" + gtf = "${params.transgenes_base}/zsGreen/zsGreen.gtf" } } } From 4491907f1461185b8be7e6906e9d7b583dc91fd3 Mon Sep 17 00:00:00 2001 From: Tobias Schraink Date: Tue, 4 Jun 2019 12:56:11 -0400 Subject: [PATCH 29/38] updated singularity version in conf/prince.config to reflect version installed on prince The prince admins changed the singularity version to 3.2.1 from 3.1.0, making the old version unavailable. To keep this config functional, I updated the version number for singularity. --- conf/prince.config | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/conf/prince.config b/conf/prince.config index 6ae4ee8..1c2ea2c 100644 --- a/conf/prince.config +++ b/conf/prince.config @@ -1,4 +1,6 @@ singularityDir = "$SCRATCH/singularity_images_nextflow" +singularityModule = "singularity/3.2.1" +squashfsModule = "squashfs/4.3" params { config_profile_description = """ @@ -17,8 +19,8 @@ singularity { process { beforeScript = """ - module load singularity/3.1.0 - module load squashfs/4.3 + module load $singularityModule + module load $squashfsModule """ .stripIndent() executor = 'slurm' From 3a481402b82debaee410afeb2b64d7ad5afd1039 Mon Sep 17 00:00:00 2001 From: Olga Botvinnik Date: Wed, 5 Jun 2019 14:42:07 -0700 Subject: [PATCH 30/38] Get czbiohub config to work --- conf/{czbiohub.config => czbiohub_aws.config} | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) rename conf/{czbiohub.config => czbiohub_aws.config} (95%) diff --git a/conf/czbiohub.config b/conf/czbiohub_aws.config similarity index 95% rename from conf/czbiohub.config rename to conf/czbiohub_aws.config index d51c6f2..baf4550 100644 --- a/conf/czbiohub.config +++ b/conf/czbiohub_aws.config @@ -20,8 +20,15 @@ docker { process { executor = 'awsbatch' + queue = 'nextflow' } +workDir = "s3://czb-nextflow/work" + +aws.region = 'us-west-2' +executor.awscli = '/home/ec2-user/miniconda/bin/aws' +params.tracedir = './' + params { saveReference = true @@ -42,7 +49,6 @@ params { // AWS configurations awsregion = "us-west-2" awsqueue = "nextflow" - workDir = "s3://czb-nextflow/rnaseq/" // GENCODE GTF and fasta files genomes { From 268e411d10eefff821625e0f72346d52cf30842e Mon Sep 17 00:00:00 2001 From: Olga Botvinnik Date: Wed, 5 Jun 2019 14:42:15 -0700 Subject: [PATCH 31/38] Add czbiohub_aws to list --- nfcore_custom.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nfcore_custom.config b/nfcore_custom.config index 7374fa0..0ca7fbe 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -16,6 +16,7 @@ profiles { ccga { includeConfig "${params.custom_config_base}/conf/ccga.config" } cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" } crick { includeConfig "${params.custom_config_base}/conf/crick.config" } + czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" } gis { includeConfig "${params.custom_config_base}/conf/gis.config" } hebbe { includeConfig "${params.custom_config_base}/conf/hebbe.config" } mendel { includeConfig "${params.custom_config_base}/conf/mendel.config" } From ad7e26ea69388a906397c41da9363a91c76c2a1c Mon Sep 17 00:00:00 2001 From: Olga Botvinnik Date: Wed, 5 Jun 2019 14:42:24 -0700 Subject: [PATCH 32/38] Write out docs for czbiohub" git push --- docs/czbiohub.md | 141 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 141 insertions(+) create mode 100644 docs/czbiohub.md diff --git a/docs/czbiohub.md b/docs/czbiohub.md new file mode 100644 index 0000000..6234fc2 --- /dev/null +++ b/docs/czbiohub.md @@ -0,0 +1,141 @@ +# nf-core/configs: CZ Biohub Configuration + +All nf-core pipelines have been successfully configured for use on the AWS Batch at the Chan Zuckerberg Biohub here. + +To use, run the pipeline with `-profile czbiohub_aws`. This will download and launch the [`czbiohub_aws.config`](../conf/czbiohub_aws.config) which has been pre-configured with a setup suitable for the AWS Batch. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. + +Ask Olga (olga.botvinnik@czbiohub.org) if you have any questions! + +## Run the pipeline from a small AWS EC2 Instance + +The pipeline will monitor and submit jobs to AWS Batch on your behalf. To ensure that the pipeline is successful, it will need to be run from a computer that has constant internet connection. Unfortunately for us, Biohub has spotty WiFi and even for short pipelines, it is highly recommended to run them from AWS. Make sure you have [aegea](https://github.com/czbiohub/codonboarding/blob/master/guides/aegea.md) installed to make launching AWS instances from the command line much easier. + +### 1. Launch the instance + +There is an Elastic Compute Cluster (EC2) Amazon machine image (AMI) set up with everything you need for Nextflow already installed. Its ID is `ami-091ec599f8e77734d` and can be launched from the command line with aegea like this: + +``` +aegea launch --iam-role S3fromEC2 -t t2.small --ami ami-091ec599f8e77734d --subnet subnet-672e832e $USER-nextflow +``` + +For example: + +``` +aegea launch --iam-role S3fromEC2 -t t2.small --ami ami-0adcc973d6f458a1e --subnet subnet-672e832e olgabot-nextflow +``` + +### 2. Log into the instance + +Log into the instance with `aegea ssh`: + +``` +aegea ssh ec2-user@$USER-nextflow +``` + +For a concrete example: + +``` +aegea ssh ec2-user@olgabot-nextflow +``` + +### 3. Start tmux + +[tmux](https://hackernoon.com/a-gentle-introduction-to-tmux-8d784c404340) is a "Terminal Multiplexer" that allows for commands to continue running even when you have closed your laptop and lost your connection. Start a new tmux session with `tmux new` + +``` +tmux new +``` + +Now you can run pipelines with abandon! + +### 4. Make a GitHub repo for your workflows (optional :) + +To make sharing your pipelines and commands easy between your teammates, it's best to share code in a GitHub repository. One way is to store the commands in a Makefile ([example](https://github.com/czbiohub/kh-workflows/blob/master/nf-kmer-similarity/Makefile)) which can contain multiple `nextflow run` commands so that you don't need to remember the S3 bucket or output directory for every single one. [Makefiles](https://kbroman.org/minimal_make/) are broadly used in the software community for running many complex commands. Makefiles can have a lot of dependencies and be confusing, so we're only going to write *simple* Makefiles. + +``` +rnaseq: + nextflow run -profile czbiohub_aws nf-core/rnaseq \ + --reads 's3://czb-maca/Plate_seq/24_month/180626_A00111_0166_BH5LNVDSXX/fastqs/*{R1,R2}*.fastq.gz' \ + --genome GRCm38 \ + --outdir s3://olgabot-maca/nextflow-test/ + +human_mouse_zebrafish: + nextflow run czbiohub/nf-kmer-similarity -latest -profile aws \ + --samples s3://kmer-hashing/hematopoeisis/smartseq2/human_mouse_zebrafish/samples.csv + + +merkin2012_aws: + nextflow run czbiohub/nf-kmer-similarity -latest --sra "SRP016501" \ + -r olgabot/support-csv-directory-or-sra \ + -profile aws +``` + +In this example, one would run the `rnaseq` rule and the nextflow command beneath it with: + +``` +make rnaseq +``` + +If one wanted to run a different command, e.g. `human_mouse_zebrafish`, they would specify that command instead. For example: + +``` +make human_mouse_zebrafish +``` + +Makefiles are a very useful way of storing longer commands with short mnemonic words. + + +Once you [create a new repository](https://github.com/organizations/czbiohub/repositories/new) (best to initialize with a `.gitignore`, license - MIT and `README`), clone that repository to your EC2 instance. For example, if the repository is called `kh-workflows`, this is what the command would look like: + +``` +git clone https://github.com/czbiohub/kh-workflows +``` + +Now both create and edit a `Makefile`: + +``` +cd +nano Makefile +``` + +Write your rule with a colon after it, and on the next line must be a **tab**, not spaces. Once you're done, exit the program (the `^` command shown in nano means "Control"), write the file, add it to git, commit it, and push it up to GitHub. + + +``` +git add Makefile +git commit -m "Added makefile" +git push origin master +``` + + +### 5. Run your workflow!! + +Remember to specify `-profile czbiohub_aws` to grab the CZ Biohub-specific AWS configurations, and an `--outdir` with an AWS S3 bucket so you don't run out of space on your small AMI + +``` +nextflow run -profile czbiohub_aws nf-core/rnaseq \ + --reads 's3://czb-maca/Plate_seq/24_month/180626_A00111_0166_BH5LNVDSXX/fastqs/*{R1,R2}*.fastq.gz' \ + --genome GRCm38 \ + --outdir s3://olgabot-maca/nextflow-test/ +``` + +### 6. If you lose connection, how do you re-attach the tmux session? + +If you close your laptop, get onto the train, or lose WiFi connection, you may lose connection to your AWS EC2 instance. To reattach, use the command `tmux attach` and you should see your Nextflow output! + +``` +tmux attach +``` + + +## iGenomes specific configuration + +A local copy of the iGenomes resource has been made available on `s3://czbiohub-reference` (in `us-west-2` region) so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. +You can do this by simply using the `--genome ` parameter. + +For Human and Mouse, we use [GENCODE](https://www.gencodegenes.org/) gene annotations. This doesn't change how you would specify the genome name, only that the pipelines run with the `czbiohub_aws` profile would be with GENCODE rather than iGenomes. + + +>NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact IT. + +>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT. From c7eed3fa4c92d92c8b5ef442d1b18df1256f4529 Mon Sep 17 00:00:00 2001 From: maxibor Date: Fri, 14 Jun 2019 19:16:20 +0200 Subject: [PATCH 33/38] fix queuesize scope and singularity --- conf/shh.config | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/conf/shh.config b/conf/shh.config index 2b195a6..5cb3396 100644 --- a/conf/shh.config +++ b/conf/shh.config @@ -8,12 +8,16 @@ params { singularity { enabled = true autoMounts = true + runOptions = '-B /run/shm:/run/shm' cacheDir = "/projects1/singularity_scratch/cache/" } process { executor = 'slurm' queue = 'short' +} + +executor { queueSize = 16 } From f40ed194e3afb9d0c6ad0c511943c404ad690cd9 Mon Sep 17 00:00:00 2001 From: Szilveszter Juhos Date: Mon, 24 Jun 2019 09:54:37 +0200 Subject: [PATCH 34/38] Using correct reference location for munin --- conf/munin.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/munin.config b/conf/munin.config index 5d95f01..bca56f7 100644 --- a/conf/munin.config +++ b/conf/munin.config @@ -28,5 +28,5 @@ params { max_cpus = 16 max_time = 72.h // illumina iGenomes reference file paths on UPPMAX - igenomes_base = '/data0/btb/references/igenomes/' + igenomes_base = '/data1/references/igenomes/' } From 45d36a150661b4f33a3847d345f17d41b74fa8ee Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 3 Jul 2019 09:21:16 +0200 Subject: [PATCH 35/38] Update cfc.config Add Weblog for CFC cluster --- conf/cfc.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/conf/cfc.config b/conf/cfc.config index dd69647..2f9047d 100644 --- a/conf/cfc.config +++ b/conf/cfc.config @@ -14,6 +14,11 @@ process { executor = 'slurm' } +weblog{ + enabled = true + url = 'http://services.qbic.uni-tuebingen.de:8080/workflows' +} + params { igenomes_base = '/nfsmounts/igenomes' max_memory = 60.GB From cb507177d5ceca20722bea2acda201c040d9300b Mon Sep 17 00:00:00 2001 From: marchoeppner Date: Fri, 5 Jul 2019 08:03:37 +0200 Subject: [PATCH 36/38] Updating CCGA config file --- conf/ccga.config | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/conf/ccga.config b/conf/ccga.config index f29db9c..b9130e0 100644 --- a/conf/ccga.config +++ b/conf/ccga.config @@ -2,15 +2,20 @@ params { config_profile_description = 'CCGA cluster profile provided by nf-core/configs.' config_profile_contact = 'Marc Hoeppner (@marchoeppner)' - config_profile_url = 'https://www.ikmb.uni-kiel.de/' + config_profile_url = 'https://www.ccga.uni-kiel.de/' } /* * ------------------------------------------------- - * Nextflow config file with environment modules for RZCluster in Kiel + * Nextflow config file for CCGA cluster in Kiel * ------------------------------------------------- */ +singularity { + enabled = true + runOptions = "-B /ifs -B /scratch -B /work_beegfs" +} + executor { queueSize=100 } @@ -29,4 +34,7 @@ params { // illumina iGenomes reference file paths on RZCluster igenomes_base = '/ifs/data/nfs_share/ikmb_repository/references/iGenomes/references/' saveReference = true + max_memory = 128.GB + max_cpus = 16 + max_time = 120.h } From d66bf4e4786799301846b34dfd9602d17c4ce3ce Mon Sep 17 00:00:00 2001 From: marchoeppner Date: Fri, 5 Jul 2019 08:28:18 +0200 Subject: [PATCH 37/38] Updating CCGA documentation --- docs/ccga.md | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 docs/ccga.md diff --git a/docs/ccga.md b/docs/ccga.md new file mode 100644 index 0000000..4a38bd9 --- /dev/null +++ b/docs/ccga.md @@ -0,0 +1,18 @@ +# nf-core/configs: CCGA Configuration + +Deployment and testing of nf-core pipelines at the CCGA cluster is on-going. + +To use, run the pipeline with `-profile ccga`. This will download and launch the [`ccga.config`](../conf/ccga.config) which has been pre-configured with a setup suitable for the BINAC cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. + +Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on the cluster. You can do this by issuing the commands below: + +```bash +## Load Nextflow and Singularity environment modules +module purge +module load IKMB +module load Java/1.8.0 +module load Nextflow +module load singularity3.1.0 +``` + +>NB: Access to the CCGA cluster is restricted to IKMB/CCGA employes. Please talk to Marc Hoeppner to get access (@marchoeppner). From fe0153befd41e7cd054a398d64dac7da89f1f45d Mon Sep 17 00:00:00 2001 From: marchoeppner Date: Fri, 5 Jul 2019 08:30:02 +0200 Subject: [PATCH 38/38] Updating CCGA documentation --- docs/ccga.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/ccga.md b/docs/ccga.md index 4a38bd9..1157cb3 100644 --- a/docs/ccga.md +++ b/docs/ccga.md @@ -2,7 +2,7 @@ Deployment and testing of nf-core pipelines at the CCGA cluster is on-going. -To use, run the pipeline with `-profile ccga`. This will download and launch the [`ccga.config`](../conf/ccga.config) which has been pre-configured with a setup suitable for the BINAC cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. +To use, run the pipeline with `-profile ccga`. This will download and launch the [`ccga.config`](../conf/ccga.config) which has been pre-configured with a setup suitable for the CCGA cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on the cluster. You can do this by issuing the commands below: