Commits · 01ba0654c6c182f02559c42c52cc1d033f84b439 · gad-public / singularity · GitLab

23 Jan, 2025 1 commit
- Modify setup and gad_version variable provision (here 2.11.0_python3) in python3.9 def file · 01ba0654
  Valentin Vautrot authored Jan 23, 2025
  
  01ba0654
17 Jan, 2025 4 commits
- Add modified-thompson-tau-test for str pipeline · 1eb92924
  Valentin Vautrot authored Jan 17, 2025
  
  1eb92924
- Add version control for python pip packages · 2f83e505
  Valentin Vautrot authored Jan 17, 2025
  
  2f83e505
- Make gad version variable available in a singularity-compatible manner and modify help · 56e48ac5
  Valentin Vautrot authored Jan 17, 2025
  
  56e48ac5
- Retrieve custom pipeline python packages from remote git clone instead of own's local repository · 5a071cbe
  Valentin Vautrot authored Jan 17, 2025
  
  5a071cbe
03 Sep, 2024 1 commit
- Add ggrepel and tidyverse packages for plotting · 68835196
  Valentin Vautrot authored Sep 03, 2024
  
  68835196
11 Jul, 2024 2 commits
- Small help section documentation correction · 577a8eba
  Valentin Vautrot authored Jul 11, 2024
  
  577a8eba
- Add DMRfinder installation + documentation and test section · 7d0f8184
  Valentin Vautrot authored Jul 11, 2024
  
  7d0f8184
04 Jul, 2024 1 commit
- Add affycoretools package · 26ff7166
  Valentin Vautrot authored Jul 04, 2024
  
  26ff7166
25 Jun, 2024 1 commit
- Add biomaRt package · eeb141e0
  Valentin Vautrot authored Jun 25, 2024
  
  eeb141e0
24 Jun, 2024 3 commits
- Correct %test section and re-add affy for testing functionalities with limma · 74f1d817
  Valentin Vautrot authored Jun 24, 2024
  
  74f1d817
- Add gcrma package for normalisation · 73b64faa
  Valentin Vautrot authored Jun 24, 2024
  
  73b64faa
- Replace affy package with oligo and add limma · 255c9638
  Valentin Vautrot authored Jun 24, 2024
  
  255c9638
21 Jun, 2024 1 commit
- Implementation of a singularity definition file to contain R with affymetrix package · 504bd6de
  Valentin Vautrot authored Jun 21, 2024
  
  504bd6de
18 Jun, 2024 1 commit
- Install GD perl module for bismark Mbiais plots · 6817ed5c
  Valentin Vautrot authored Jun 18, 2024
  
  6817ed5c
13 Jun, 2024 1 commit
- Creation of bismark definition file · 7568d221
  Valentin Vautrot authored Jun 13, 2024
  
  7568d221
06 May, 2024 1 commit
- Add R version contol + results annotation tools for Fraser sif image · df87ddf2
  Valentin Vautrot authored May 06, 2024
  
  df87ddf2
27 Mar, 2024 1 commit
- Initial implementation of R definition file to run R program for mouse chipseq… · 2d5aaa5b
  Valentin Vautrot authored Mar 27, 2024
```
Initial implementation of R definition file to run R program for mouse chipseq analysis (chipseq_mm10.R)
```
  2d5aaa5b
22 Mar, 2024 2 commits
- Cleaning up .def file script and useless comments · ffa4d431
  Valentin Vautrot authored Mar 22, 2024
  
  ffa4d431
- Add R installation in picard singularity image · 7d92b402
  Valentin Vautrot authored Mar 22, 2024
  
  7d92b402
06 Mar, 2024 2 commits
- Add TODO comment to test removal of unnecessary installations · 2ccc7aab
  Valentin Vautrot authored Mar 06, 2024
  
  2ccc7aab
- First implementation of Singularity image definition file for FRASER · 93a6da47
  Valentin Vautrot authored Mar 06, 2024
  
  93a6da47
22 Nov, 2023 6 commits
- Suppress useless comment lines · 8709ca27
  Valentin Vautrot authored Nov 22, 2023
  
  8709ca27
- Add authors in labels section · a7603718
  Valentin Vautrot authored Nov 22, 2023
  
  a7603718
- Add test section, labels, clean-up and annotations · 6ecf7d9c
  Valentin Vautrot authored Nov 22, 2023
  
  6ecf7d9c
- Minor modifications in annotations and help · 9812b3fe
  Valentin Vautrot authored Nov 22, 2023
  
  9812b3fe
- Minor modifications in annotations and help · 46eddb40
  Valentin Vautrot authored Nov 22, 2023
  
  46eddb40
- Create definition file for singularity image dedicated to R analysis using OUTRIDER · 18ad533c
  Valentin Vautrot authored Nov 22, 2023
  
  18ad533c
17 Nov, 2023 1 commit
- Adding R3.4 singularity definition · 39ace5bb
  Yannis Duffourd authored Nov 17, 2023
  
  39ace5bb
05 Oct, 2023 1 commit
- Add more detail to %help section, simplify and correct %labels and %test section · c636cfd7
  Valentin Vautrot authored Oct 05, 2023
  
  c636cfd7
03 Oct, 2023 1 commit
- suppressing useless packages and adding OS version info · ec5e1c7c
  Valentin Vautrot authored Oct 03, 2023
  
  ec5e1c7c
29 Sep, 2023 2 commits
- adding info in %labels and %help sections · 6f5a90de
  Valentin Vautrot authored Sep 29, 2023
  
  6f5a90de
- cleaning unecessary command lines for previous installations attempts (rmats, lumpy) · 0d67915e
  Valentin Vautrot authored Sep 29, 2023
  
  0d67915e
28 Sep, 2023 1 commit
- Added all python packages needed to run full_wes.sh, full_wgs.sh and… · 0cd8b53e
  Valentin Vautrot authored Sep 28, 2023
```
Added all python packages needed to run full_wes.sh, full_wgs.sh and full_RNAseq.sh, and trying to install lumpy
```
  0cd8b53e
26 Sep, 2023 1 commit
- Added rMATS installation and required environment for full_rna.sh · 03275bbd
  Valentin Vautrot authored Sep 26, 2023
  
  03275bbd
18 Sep, 2023 1 commit
- Added python 3.9 packages installation verified up until the end of full_wes.sh… · 29b6c61d
  Valentin Vautrot authored Sep 18, 2023
```
Added python 3.9 packages installation verified up until the end of full_wes.sh as in version 2.10.0 of gadpipeline
```
  29b6c61d
15 Sep, 2023 1 commit
- Added python 3.9 packages installation up until the end of the CNV section in full_wes v.2.10.0 · 1c716329
  Valentin Vautrot authored Sep 15, 2023
  
  1c716329
14 Sep, 2023 3 commits
- Added python 3.9 packages installation up until the end of the mito pipeline in full_wes v.2.10.0 · 61c38963
  Valentin Vautrot authored Sep 14, 2023
  
  61c38963
- Update python_3.9 · 19b5fe24
  Valentin Vautrot authored Sep 14, 2023
  
  19b5fe24
- Update Python3.11_wes.def · 7b5795e4
  Valentin Vautrot authored Sep 14, 2023
  
  7b5795e4