Diffusion eSCT pipeline interoperability (master) History

History
master3279c9f29cb286880ec9329…

Nov 27 2017

Dry-run functionality
3279c9f29cb2
·kashev on Nov 27 2017, 17:50.
Template command
59f3b2b72af7
·kashev on Nov 27 2017, 15:36.

Oct 13 2017

Updates after testing
806dde518604
·laurenczy on Oct 13 2017, 13:03.
Added different configurations
a6553f67ba20
·laurenczy on Oct 13 2017, 10:32.
Changing build and run scripts to separate steps
467127cb1972
·laurenczy on Oct 13 2017, 10:19.
Bugfixes
a5554b2887ea
·laurenczy on Oct 13 2017, 10:18.
Bugfixes
43f797536bbb
·laurenczy on Oct 13 2017, 10:15.
Added python + cuda config
79b8de8cf215
·laurenczy on Oct 13 2017, 10:12.
Added python + cuda config
0156083bd4f3
·laurenczy on Oct 13 2017, 10:10.
Updates for testing
d040f01e1881
·laurenczy on Oct 13 2017, 09:54.
Updates for testing
bc3c23a87406
·laurenczy on Oct 13 2017, 09:53.
Updating runner config file
db6b13fa31bd
·laurenczy on Oct 13 2017, 09:40.
Updated building and running scripts
688462c08f42
·laurenczy on Oct 13 2017, 09:38.

Oct 12 2017

Updated Dockerfiles for cudnn library
a00fd86c981d
·laurenczy on Oct 12 2017, 18:31.
Updated Singularity images runner script to test for tensorflow
11692fe2863b
·laurenczy on Oct 12 2017, 16:37.
Updated LD_LIBRARY_PATH definitions
bea67b54dc79
·laurenczy on Oct 12 2017, 16:30.
Updated running script
a80b2c1c0190
·laurenczy on Oct 12 2017, 16:26.
Added test script and running script
67fe47664b4c
·laurenczy on Oct 12 2017, 16:24.
Updating pulling script
b9bf6c0eddc6
·laurenczy on Oct 12 2017, 16:18.
Added GPU Dockerfiles
74e80d38f60d
·laurenczy on Oct 12 2017, 16:09.

Aug 25 2017

Changing the container creation
17a6f64dceac
·laurenczy on Aug 25 2017, 12:44.

Aug 23 2017

Adding MPI over ethernet submission scripts
619ccbcf7002
·laurenczy on Aug 23 2017, 14:10.
Adding MPI over ethernet submission scripts
13fc090e376c
·laurenczy on Aug 23 2017, 14:09.
Merge branch 'master' of ssh://c4science.ch/diffusion/2915/esct-pipeline…
055030e15783
·laurenczy on Aug 23 2017, 11:12.
Removing temporary notes file
2aad49e7de90
·laurenczy on Aug 23 2017, 11:11.
Removing bad logs
bc45aa9e34a6
·laurenczy on Aug 23 2017, 10:42.
Added LSF sumbission logs
862c01026060
·laurenczy on Aug 23 2017, 10:39.
Added tilling submission scripts
dd79edaa35d9
·laurenczy on Aug 23 2017, 09:10.

Aug 22 2017

Fixing CUDA parameter in submission scripts
f5be7e83ff6e
·laurenczy on Aug 22 2017, 17:25.
Updating launching script
65cee79109aa
·laurenczy on Aug 22 2017, 17:22.
Updating launching script
6e41f720c7c9
·laurenczy on Aug 22 2017, 17:20.
Added LSF job launching script
216ef40c4fec
·laurenczy on Aug 22 2017, 17:18.
Added no CUDA versions of LSF scripts
a542b873640b
·laurenczy on Aug 22 2017, 17:13.
Added .out extension to log files
f83d3a7bb197
·laurenczy on Aug 22 2017, 17:08.
Added no container script
61d8604e0874
·laurenczy on Aug 22 2017, 17:07.
Merge branch 'master' of https://c4science.ch/diffusion/2915/esct-pipeline…
5f87b95ca8ed
·laurenczy on Aug 22 2017, 17:05.
Added Singularity build scritp
fc109dd6439d
·laurenczy on Aug 22 2017, 17:03.
Added LSF submission scripts
4b2d7443f497
·laurenczy on Aug 22 2017, 17:02.
Fixed version number
1bd341d02d96
·laurenczy on Aug 22 2017, 16:00.
Fixed version number
06e90b3f25ec
·laurenczy on Aug 22 2017, 15:58.
Added pushing script
96b5a036c592
·laurenczy on Aug 22 2017, 15:20.
Fixed Dockerfile for LD_LIBRARY_PATH and PATH variables
5ab0f7969cb5
·laurenczy on Aug 22 2017, 15:10.
Added docker images building script
974c8ef4235c
·laurenczy on Aug 22 2017, 15:08.
Deleting logs from repo
98bb54e0f689
·laurenczy on Aug 22 2017, 15:04.
Ordering files, renaming, adding comments
c32b5b9f3aa0
·laurenczy on Aug 22 2017, 15:01.

Aug 14 2017

Added Dockerfile and YAML file
06a1296c950b
·laurenczy on Aug 14 2017, 16:25.
Added MPI folder
286888735b82
·laurenczy on Aug 14 2017, 15:56.

Jul 20 2017

Packaged for PyPi
1bcec4e2b0e1
·kashev on Jul 20 2017, 16:55.
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.

Historymaster3279c9f29cb286880ec9329…

Nov 27 2017

Oct 13 2017

Oct 12 2017

Aug 25 2017

Aug 23 2017

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Jun 9 2017

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Jun 1 2017

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May 22 2017

May 19 2017

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Apr 28 2017

Apr 21 2017

Mar 24 2017

History
master3279c9f29cb286880ec9329…