Diffusion eSCT pipeline interoperability (master) History

History
master25877569f9e07cc81f1785b…

Jul 20 2017

Added docker2singularity build type; binds; {run}/{exec}
25877569f9e0
·kashev on Jul 20 2017, 15:33.

Jul 17 2017

Binds section, refactor substitutions
1de174bfdd99
·kashev on Jul 17 2017, 18:12.

Jul 7 2017

Added HTML validation
b80d3d163280
·• sduvaud on Jul 7 2017, 14:25.

Jun 28 2017

removed wrapper.sh which is already in container"
1dd1e2c8127b
·heinzstockinger on Jun 28 2017, 09:50.
added SIB-publications example
072d723992fe
·Heinz Stockinger on Jun 28 2017, 08:26.

Jun 23 2017

Added config file for hello_world
41139a0fa5b1
·laurenczy on Jun 23 2017, 16:56.
Tested runner script, made a python3 version
f5ec274b5772
·laurenczy on Jun 23 2017, 16:22.

Jun 22 2017

Merge branch 'master' of ssh://c4science.ch/diffusion/2915/esct-pipeline…
2dda3e0d84ca
·kashev on Jun 22 2017, 17:25.
First version of pipeline runner script. Still WIP but functional, with…
6f09d9c943be
·kashev on Jun 22 2017, 17:24.
Added own version of docker2singularity to try to reduce size of converted image
87ebc08e65e2
·laurenczy on Jun 22 2017, 16:12.
Added tests for hello world light
917c7dbef8a7
·laurenczy on Jun 22 2017, 16:11.

Jun 14 2017

Changing LSF submission scripts for pipeline1 (more memory)
5312e3ee74a5
·laurenczy on Jun 14 2017, 14:47.
Changing LSF submission scripts for pipeline1 (more memory)
dc47940dd1f2
·laurenczy on Jun 14 2017, 12:43.
Changing LSF submission scripts for pipeline1
05ccf8c0695c
·laurenczy on Jun 14 2017, 10:18.

Jun 13 2017

Changing LSF submission scripts
a26dfaf7ef80
·laurenczy on Jun 13 2017, 17:19.
Changing LSF submission scripts
ba52ee6fa89f
·laurenczy on Jun 13 2017, 16:35.
Added bowtie2 installation to pipeline2 Dockerfile
c7b9f3ad048f
·laurenczy on Jun 13 2017, 16:31.
Testing pipelines with singularity pull
f45978fdd4bb
·laurenczy on Jun 13 2017, 16:19.

Jun 12 2017

Testing private GitLab (1)
630423d182f8
·laurenczy on Jun 12 2017, 11:10.

Jun 9 2017

First pipeline. Not tested
03a5875e56d2
·• sduvaud on Jun 9 2017, 15:43.
Adapting Pablo's pipeline #2 to Vital-it
21e422a4ed5e
·• sduvaud on Jun 9 2017, 14:43.

Jun 8 2017

define the singularity container as a variable
cb2b6168f33f
·Pablo Escobar on Jun 8 2017, 15:52.
some style fixes in the submit scripts
10da60ad112f
·Pablo Escobar on Jun 8 2017, 15:36.
use modules to load Singularity
dc1a57f4a561
·Pablo Escobar on Jun 8 2017, 15:25.

Jun 1 2017

Added Dockerfile for pipeline2 and some scripts, started pipeline1 snakemake…
bc74245c0363
·laurenczy on Jun 1 2017, 14:09.

May 30 2017

Updated the hello world pipeline. Provided download link for the Singularity…
21ff5170b17d
·laurenczy on May 30 2017, 14:57.
BugFix for pipeline1
14c3d834a9d5
·laurenczy on May 30 2017, 10:46.
Changing parameters for pipeline1
a137d06ae1a0
·laurenczy on May 30 2017, 10:31.
Changing parameters for pipeline1
4e03d975d3e8
·laurenczy on May 30 2017, 10:28.
Changing parameters for pipeline1
05611b7b8bbd
·laurenczy on May 30 2017, 10:24.
Changing parameters for pipeline1
623b95a9f0cf
·laurenczy on May 30 2017, 10:24.

May 29 2017

Adapted submission script to LSF (running on Euler) for pipeline2
645b3e1d6f40
·laurenczy on May 29 2017, 17:00.
Adapted submission script to LSF (running on Euler)
5f9551340c48
·laurenczy on May 29 2017, 16:45.
Changing folder structure
b6c0776b9425
·laurenczy on May 29 2017, 16:33.

May 24 2017

updated README files with the right download urls
48986a51e8d8
·Pablo Escobar on May 24 2017, 14:09.
added vcftools to the singularity bootstrap file
abd314c44cfa
·Pablo Escobar on May 24 2017, 11:51.

May 22 2017

renamed output log
ba029b9382ca
·Pablo Escobar on May 22 2017, 17:32.
added bootstrap file and submit script using containers for pipeline2
6116ad61478a
·Pablo Escobar on May 22 2017, 16:51.

May 19 2017

added submit scripts without containers for pipeline2
5b9e8cc39cdc
·Pablo Escobar on May 19 2017, 16:58.
udpate README with the url to download the singularity container
f7b55cb712f3
·Pablo Escobar on May 19 2017, 15:36.
renamed README file
d35eeca0493d
·Pablo Escobar on May 19 2017, 15:35.
added submit script using singularity containers
1c1d706558d8
·Pablo Escobar on May 19 2017, 15:34.
update submit script without containers to use a different output dir
0c09cee61b87
·Pablo Escobar on May 19 2017, 15:34.
first commit for pipeline1
b06c9dfdf23c
·Pablo Escobar on May 19 2017, 11:38.

May 2 2017

Small fixes
b590df206853
·laurenczy on May 2 2017, 08:41.

Apr 28 2017

Testing scicore pipeline...
f9d26fef981b
·laurenczy on Apr 28 2017, 18:07.
Updating pipelines, work in progress...
65c2a27f3f55
·laurenczy on Apr 28 2017, 17:03.
Renaming pipelines, adding tests for sciCORE's pipeline
bb36f5cef5b2
·laurenczy on Apr 28 2017, 16:55.

Apr 21 2017

Added first version of the basic 'hello world' pipeline
42362601403b
·laurenczy on Apr 21 2017, 15:42.

Mar 24 2017

Added SIS folder
86f5e6f22b31
·laurenczy on Mar 24 2017, 13:30.
initial commit
7e568b720017
·laurenczy on Mar 24 2017, 13:27.

Historymaster25877569f9e07cc81f1785b…

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History
master25877569f9e07cc81f1785b…