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884 commits

Author SHA1 Message Date
MaxUlysse
332ba0dadb fix: update and rearrange munin configuration file and docs 2019-08-07 11:10:48 +02:00
Martin Proks
c583aa0233 Added kraken config (#15) 
* Added kraken template
* docs: updated some info
* fix: updated igenomes_base path
 2019-08-05 11:19:05 +02:00
drpatelh
e0c684ee8f Aarrrgh pulling configs from master 2019-07-31 23:39:42 +01:00
drpatelh
a692ded933 Remove workDir in czbiohub 2019-07-31 23:30:51 +01:00
drpatelh
daf1b9dcd2 Fix type in uppmax-devel 2019-07-31 22:09:30 +01:00
Remi Planel
1c0d596582 Merge remote-tracking branch 'upstream/master' 2019-07-30 16:15:20 +02:00
Remi Planel
b4cffe0455 Remove buggy cluster option 2019-07-30 15:15:07 +02:00
marchoeppner
b31db18dfb Adding config file for CCGA dx cluster 2019-07-29 12:08:07 +02:00
Remi Planel
fbb33fde63 Details 2019-07-24 11:43:08 +02:00
Remi Planel
1b30c5a4d2 Add the Pasteur profile 2019-07-24 11:32:02 +02:00
Alexander Peltzer
9106559b2f
Update cfc.config 2019-07-15 17:53:11 +02:00
Olga Botvinnik
474e98daaf
Merge branch 'master' into olgabot/czb-update 2019-07-09 16:02:25 -07:00
marchoeppner
cb507177d5 Updating CCGA config file 2019-07-05 08:03:37 +02:00
Olga Botvinnik
069963ff8a Make czbiohub_aws_highpriority only set the AWS Batch queue and nothing else 2019-07-03 16:01:47 -07:00
Olga Botvinnik
917ec0863d add default trimming 2019-07-03 16:01:03 -07:00
Alexander Peltzer
45d36a1506
Update cfc.config 
Add Weblog for CFC cluster
 2019-07-03 09:21:16 +02:00
Olga Botvinnik
6a2d2003f0 Add high priority AWS batch queue to CZBiohub AWS 2019-07-01 09:25:46 -07:00
Olga Botvinnik
70b5205d15 Add human salmon index and mouse star index 2019-06-27 15:02:47 -07:00
Olga Botvinnik
d1983f8acd Use new and improved GENCODE+ERCC annotation 2019-06-26 17:56:26 -07:00
Olga Botvinnik
b0c67e0a9b Add both seqCenter and seq_center 2019-06-24 17:52:10 -07:00
Olga Botvinnik
acad9ac7e5 Try to clean up czb update 2019-06-24 17:50:36 -07:00
Szilveszter Juhos
f40ed194e3 Using correct reference location for munin 2019-06-24 09:54:37 +02:00
James A. Fellows Yates
505af9a909
Merge pull request #49 from maxibor/master 
Fix queuesize Ccope and Singularity
 2019-06-18 20:36:36 +02:00
maxibor
c7eed3fa4c fix queuesize scope and singularity 2019-06-14 19:16:20 +02:00
Alexander Peltzer
ebe838ac7e
Merge pull request #45 from czbiohub/olgabot/czbiohub 
[WIP] Add CZ Biohub
 2019-06-06 13:35:34 +02:00
Olga Botvinnik
3a481402b8 Get czbiohub config to work 2019-06-05 14:42:07 -07:00
Tobias Schraink
4491907f14 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.
 2019-06-04 12:56:11 -04:00
Alexander Peltzer
515e9484de
Merge pull request #44 from drpatelh/dev 
Add proper nf-core logo
 2019-06-01 12:36:57 +02:00
Olga Botvinnik
9c0315addb Use flat nongzipped files 2019-05-31 13:17:48 -07:00
Olga Botvinnik
1b2fcf5a98 Add author lines 2019-05-31 08:16:51 -07:00
Olga Botvinnik
66eeeebe81 Initial commit of CZBiohub 2019-05-30 11:15:38 -07:00
Alexander Peltzer
441ddbcdab
Newest Update is 3.0.3 2019-05-28 15:25:10 +02:00
maxibor
de1b2aa7d2 remove autoformat added space 2019-04-25 15:50:48 +02:00
maxibor
efd831a8a3 add automounts for singularity 2019-04-25 15:48:20 +02:00
Alexander Peltzer
7d7c18273b
Merge pull request #41 from tobsecret/master 
Added configs for NYU clusters BigPurple (NYU Med) and Prince (NYU main campus)

Last PR merge before Easter holiday ;-)
 2019-04-19 00:13:49 +02:00
Tobias Schraink
4ba831705d added nyu prince and bigpurple md files, added singularity cacheDir to prince and bigpurple configs 2019-04-18 14:13:02 -04:00
maxibor
9d9ac4c3bb remove whitespace 2019-04-18 11:22:54 +02:00
maxibor
1772f4119c adding igenomes to shh config 2019-04-18 11:19:53 +02:00
Tobias Schraink
4a915e330a added warnings to run on SCRATCH 2019-04-17 17:15:16 -04:00
Tobias Schraink
51c2a54399 added nyu prince and bigpurple configs 2019-04-17 16:59:38 -04:00
maxibor
76a5fcf077 switch to queueSize 16 for shh config 2019-03-20 13:44:13 +01:00
maxibor
0929349303 add queueSize limited to 5 2019-03-18 11:13:11 +01:00
James A. Fellows Yates
ecb36dd8c2
Reduced memory and CPUs for cdag compatibility 
Also matches 'fair use' policy
 2019-03-14 21:26:43 +01:00
James A. Fellows Yates
3da1373c14
Updated path to centralised singularity cache 2019-03-14 21:16:02 +01:00
Harshil Patel
8bc975c8c3
Merge pull request #33 from ewels/master 
Removed params.config_profile_name, added params.hostnames
 2019-03-13 16:49:43 +00:00
Phil Ewels
1191863e1c Removed params.config_profile_name, added params.hostnames 2019-03-13 17:19:34 +01:00
phue
13df59bfaf remove singularity support 
reasons:

* the kernel running on the compute nodes does not support overlayfs und thus containers downloaded from
  public registries won't run because they lack the /lustre mountpoint

* building containers manually using the Singularity file would work, however nf-core pipelines will stop
  providing these files in future releases
 2019-03-12 17:57:31 +00:00
Alexander Peltzer
fbf9397182 Bump 2019-03-12 18:48:29 +01:00
Alexander Peltzer
3ee7195fa8 Central resource for both binac and cfc now 2019-03-12 14:58:41 +01:00
Alexander Peltzer
68b759d6ef Mini Update 2019-03-11 18:12:35 +01:00
Alexander Peltzer
f4f3c4e53b Roll out binac too 2019-03-11 14:29:42 +01:00
Alexander Peltzer
6b21538062 Rolling out iGenomes now 2019-03-07 16:12:30 +01:00
phue
59887d9bc8 update config for MENDEL cluster 2019-02-27 16:03:26 +00:00
Alexander Peltzer
164ae59568
Update cfc.config 
Please use the newest singularity version 3.0.3!
 2019-02-21 10:49:29 +01:00
Alexander Peltzer
d6ea834f40
Update cfc.config 2019-02-21 09:17:28 +01:00
Alexander Peltzer
637ffb782c
Fix CFC config 2019-02-19 17:03:53 +01:00
James A. Fellows Yates
7a51c684f5
Made small SLURM queue change for SHH 2019-01-21 20:31:37 +01:00
Martin Proks
7acd9cf7df
Updating suggested changes 2019-01-11 15:28:10 +01:00
Martin Proks
89dbb6c061
Setting Singularity as default method 2019-01-11 14:37:12 +01:00
Martin Proks
548c8bca3f
Updated munin doc and configuration 2019-01-10 15:46:16 +01:00
Martin Proks
f259178642
Added munin config boilerplate 2019-01-09 17:27:55 +01:00
Phil Ewels
66a08891c7 Documentation tweaks 2019-01-07 14:25:06 +01:00
Harshil Patel
59bc3b43be
Update crick.config 2019-01-07 11:35:49 +00:00
Harshil Patel
f81c67627e
Update crick.config 2019-01-07 11:18:01 +00:00
Alexander Peltzer
d4ea56aaae Update UCT_Hex profile 2019-01-07 12:14:04 +01:00
Alexander Peltzer
2b814041ee Add in both uppmax profiles 2019-01-04 16:33:54 +01:00
Alexander Peltzer
6f7a3cc422 Add Hebbe 2019-01-04 16:30:40 +01:00
Alexander Peltzer
e07d8bd687 Get rid of header in CRICK config 2019-01-04 16:29:49 +01:00
Alexander Peltzer
aca790bb4b Add CCGA Profile 2019-01-04 16:28:41 +01:00
Alexander Peltzer
7af6b48b4d Adjust general usage to separate params section 2019-01-04 14:55:22 +01:00
Alexander Peltzer
9c97680d4c Add UZH 2019-01-04 14:49:52 +01:00
Alexander Peltzer
bc8e05f4b3 Add Phoenix 2019-01-04 14:48:14 +01:00
Alexander Peltzer
6ae7d02b14 Add Mendel 2019-01-04 14:46:30 +01:00
Alexander Peltzer
078272745a Update BINAC, CFC, SHH COnfig profiles 2019-01-04 14:42:09 +01:00
Alexander Peltzer
87cea82c43 Use james github handle 2019-01-04 10:21:16 +01:00
Alexander Peltzer
a78fe147f0 Add more details on config profiles 2019-01-04 10:19:39 +01:00
Alexander Peltzer
1051339461 Remove base config stuff 2019-01-03 16:02:07 +01:00
Alexander Peltzer
98fca8a1ef Add SHH Configuration 2019-01-03 16:01:06 +01:00
phue
5c609859c5 add config for MENDEL cluster 2018-12-04 16:58:33 +01:00
Harshil Patel
ddc0bbd7b3
Update phoenix.config 2018-11-26 23:31:44 +00:00
Alexander Peltzer
42ed4b9da4 Add Phoenix configs 2018-11-27 00:02:40 +01:00
Harshil Patel
2c513e5266
Update binac.config 2018-11-26 22:47:36 +00:00
Phil Ewels
e38e9327f4 Some tidying 2018-11-26 17:32:06 +01:00
drpatelh
d52db66077 Added existing configs from all pipelines 2018-11-23 15:56:34 +00:00