From 8a9d3ad8a0ca66ef35276adacc1facac4d1b0129 Mon Sep 17 00:00:00 2001 From: Evan Floden Date: Fri, 6 Mar 2020 05:47:29 +0000 Subject: [PATCH 1/5] First commit of Google Cloud config --- .github/workflows/main.yml | 2 +- README.md | 1 + conf/google.config | 21 +++++++++++++++++++++ docs/google.md | 30 ++++++++++++++++++++++++++++++ docs/images/google-cloud-logo.png | Bin 0 -> 13226 bytes nfcore_custom.config | 1 + 6 files changed, 54 insertions(+), 1 deletion(-) create mode 100644 conf/google.config create mode 100644 docs/google.md create mode 100644 docs/images/google-cloud-logo.png diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 5fb2601..d68f44f 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: matrix: - profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh'] + profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'google', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh'] steps: - uses: actions/checkout@v1 - name: Install Nextflow diff --git a/README.md b/README.md index 0e58b09..b49edb7 100644 --- a/README.md +++ b/README.md @@ -108,6 +108,7 @@ Currently documentation is available for the following systems: * [GENOTOUL](docs/genotoul.md) * [GENOUEST](docs/genouest.md) * [GIS](docs/gis.md) +* [GOOGLE](docs/google.md) * [HEBBE](docs/hebbe.md) * [KRAKEN](docs/kraken.md) * [MUNIN](docs/munin.md) diff --git a/conf/google.config b/conf/google.config new file mode 100644 index 0000000..4333d86 --- /dev/null +++ b/conf/google.config @@ -0,0 +1,21 @@ +// Nextflow config file for running on Google Cloud Life Sciences +params { + config_profile_description = 'Google Cloud Life Sciences Profile' + config_profile_contact = 'Evan Floden, Seqera Labs (@evanfloden)' + config_profile_url = 'https://cloud.google.com/life-sciences' + + google_zone = 'europe-west2-c' + google_bucket = false + google_debug = false + google_preemptible = true +} + +process.executor = 'google-lifesciences' +google.zone = params.google_zone +google.lifeSciences.debug = params.google_debug +workDir = params.google_bucket +google.lifeSciences.preemptible = params.google_preemptible +if (google.lifeSciences.preemptible) { + process.errorStrategy = { task.exitStatus==14 ? 'retry' : 'terminate' } + process.maxRetries = 5 +} \ No newline at end of file diff --git a/docs/google.md b/docs/google.md new file mode 100644 index 0000000..d2b0f51 --- /dev/null +++ b/docs/google.md @@ -0,0 +1,30 @@ +# nf-core/configs: Google Cloud Life Sciences Configuration +![Google Cloud](images/google-cloud-logo.png "https://cloud.google.com/life-sciences/docs/tutorials/nextflow") + +To be used with the `google` profile by specifying the `-profile google` when running nf-core pipelines. + +## Quick Start +``` +GOOGLE_APPLICATION_CREDENTIALS=.json +NXF_MODE=google +nextflow run nf-core/rnaseq -profile google,test --google_bucket +``` + +## Required Parameters +#### `--google-bucket` +The Google Cloud Storage bucket location to be used as a Nextflow work directory. Can also be specified with (`-w gs://your_bucket/work`). + +## Optional Parameters +#### `--google-zone` +The Google zone where the computation is executed in Compute Engine VMs. Multiple zones can be provided separating them by a comma. Default (`europe-west2-c`). + +#### `--google-preemptible` +Enables the usage of preemptible virtual machines with a retry error statergy for up to 5 retries. Default (`true`) + +#### `--google-debug` +Copies the /google debug directory from the VM to the task bucket directory. Useful for debugging. Default (`false`). + +## Google Cloud Life Sciences Setup +Please refer to the [Google Cloud](https://cloud.google.com/life-sciences/docs/tutorials/nextflow) and [Nextflow](https://www.nextflow.io/docs/latest/google.html#cloud-life-sciences) documentation which describe how to setup the Google Cloud environment. + + diff --git a/docs/images/google-cloud-logo.png b/docs/images/google-cloud-logo.png new file mode 100644 index 0000000000000000000000000000000000000000..07c9a325b254d93f3fe4e94abb5cbdd9162afd92 GIT binary patch literal 13226 zcmZ{LWmFtZ(C#em?hxEvg9ZyO!QI^@xVuYm4=%yoC1}tM9^5SicY=SL_ulWE`{$lL zXJ=-&d#0zlx}K`1s-u-ZNuweWAprn@Dk~$Q3IL!R$oVG(ILP;Q0N3;+U|0D$lOwNph1@&}x$ytD-H z_U}{B^DPAcIQwNK#MHf3P7S>M)HLqi@}81wmEYs5zsGzhZJ`2#uReZsc4)m;peQ4k zt$ExYPjv_$LiN<2e$S$qjdNeQ`-MDb_x&r*y}Q1su{kCNJ&Qw%=hS(EX4w048bw2` zjeD-YS?}w3@AEv*U-DefI(}maP%I%g?61#Amtzt^570xQ!a1`CiIJOg3y0+a>Oc<2 z9_~_#-Ct>IihAxhwVjBd@sA8alYuZqY+8jA=z_`Fq+2V}u3l9q{>Z4;p)Ew9Fl+pts3YF0?dq9pjU|kyJuiE?tw!fxd 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insertions(+), 5 deletions(-) delete mode 100644 docs/images/google-cloud-logo.png create mode 100644 docs/images/google-cloud-logo.svg diff --git a/docs/google.md b/docs/google.md index d2b0f51..d3a65f5 100644 --- a/docs/google.md +++ b/docs/google.md @@ -1,8 +1,11 @@ # nf-core/configs: Google Cloud Life Sciences Configuration -![Google Cloud](images/google-cloud-logo.png "https://cloud.google.com/life-sciences/docs/tutorials/nextflow") To be used with the `google` profile by specifying the `-profile google` when running nf-core pipelines. + +![Google Cloud](images/google-cloud-logo.svg "https://cloud.google.com/life-sciences/docs/tutorials/nextflow") + + ## Quick Start ``` GOOGLE_APPLICATION_CREDENTIALS=.json @@ -10,21 +13,22 @@ NXF_MODE=google nextflow run nf-core/rnaseq -profile google,test --google_bucket ``` -## Required Parameters +### Required Parameters #### `--google-bucket` The Google Cloud Storage bucket location to be used as a Nextflow work directory. Can also be specified with (`-w gs://your_bucket/work`). -## Optional Parameters +### Optional Parameters #### `--google-zone` The Google zone where the computation is executed in Compute Engine VMs. Multiple zones can be provided separating them by a comma. Default (`europe-west2-c`). #### `--google-preemptible` -Enables the usage of preemptible virtual machines with a retry error statergy for up to 5 retries. Default (`true`) +Enables the usage of preemptible virtual machines with a retry error statergy for up to 5 retries. Default (`true`). #### `--google-debug` Copies the /google debug directory from the VM to the task bucket directory. Useful for debugging. Default (`false`). -## Google Cloud Life Sciences Setup + +## Cloud Life Sciences Setup Please refer to the [Google Cloud](https://cloud.google.com/life-sciences/docs/tutorials/nextflow) and [Nextflow](https://www.nextflow.io/docs/latest/google.html#cloud-life-sciences) documentation which describe how to setup the Google Cloud environment. diff --git a/docs/images/google-cloud-logo.png b/docs/images/google-cloud-logo.png deleted file mode 100644 index 07c9a325b254d93f3fe4e94abb5cbdd9162afd92..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 13226 zcmZ{LWmFtZ(C#em?hxEvg9ZyO!QI^@xVuYm4=%yoC1}tM9^5SicY=SL_ulWE`{$lL zXJ=-&d#0zlx}K`1s-u-ZNuweWAprn@Dk~$Q3IL!R$oVG(ILP;Q0N3;+U|0D$lOwNph1@&}x$ytD-H z_U}{B^DPAcIQwNK#MHf3P7S>M)HLqi@}81wmEYs5zsGzhZJ`2#uReZsc4)m;peQ4k zt$ExYPjv_$LiN<2e$S$qjdNeQ`-MDb_x&r*y}Q1su{kCNJ&Qw%=hS(EX4w048bw2` zjeD-YS?}w3@AEv*U-DefI(}maP%I%g?61#Amtzt^570xQ!a1`CiIJOg3y0+a>Oc<2 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6 Mar 2020 09:48:00 +0100 Subject: [PATCH 3/5] Alphabetical ordering of GitHub workflows --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index d68f44f..5e9676d 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: matrix: - profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'google', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh'] + profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh'] steps: - uses: actions/checkout@v1 - name: Install Nextflow From f5364e45e7c007d9da5b24dcb50c5329b53b36ae Mon Sep 17 00:00:00 2001 From: Evan Floden Date: Fri, 6 Mar 2020 11:27:44 +0100 Subject: [PATCH 4/5] Update google.md or markdown linting --- docs/google.md | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/docs/google.md b/docs/google.md index d3a65f5..0534a0b 100644 --- a/docs/google.md +++ b/docs/google.md @@ -2,33 +2,36 @@ To be used with the `google` profile by specifying the `-profile google` when running nf-core pipelines. - ![Google Cloud](images/google-cloud-logo.svg "https://cloud.google.com/life-sciences/docs/tutorials/nextflow") - ## Quick Start -``` + +```bash GOOGLE_APPLICATION_CREDENTIALS=.json NXF_MODE=google nextflow run nf-core/rnaseq -profile google,test --google_bucket ``` ### Required Parameters + #### `--google-bucket` + The Google Cloud Storage bucket location to be used as a Nextflow work directory. Can also be specified with (`-w gs://your_bucket/work`). ### Optional Parameters + #### `--google-zone` + The Google zone where the computation is executed in Compute Engine VMs. Multiple zones can be provided separating them by a comma. Default (`europe-west2-c`). #### `--google-preemptible` + Enables the usage of preemptible virtual machines with a retry error statergy for up to 5 retries. Default (`true`). #### `--google-debug` + Copies the /google debug directory from the VM to the task bucket directory. Useful for debugging. Default (`false`). - ## Cloud Life Sciences Setup + Please refer to the [Google Cloud](https://cloud.google.com/life-sciences/docs/tutorials/nextflow) and [Nextflow](https://www.nextflow.io/docs/latest/google.html#cloud-life-sciences) documentation which describe how to setup the Google Cloud environment. - - From ebae81ceb3a5a9d07d72d31b33867a369944d889 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 6 Mar 2020 17:18:03 +0100 Subject: [PATCH 5/5] Update main.yml Drop CCGA, as it was removed in an intermediate merge. --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 5e9676d..36f9da1 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: matrix: - profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh'] + profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh'] steps: - uses: actions/checkout@v1 - name: Install Nextflow