Commits · 7f6056dcc44a008640d91b3c1a3a2db7f151d30b · Blaise LI / bioinfo_utils

18 Dec, 2019 1 commit
- Fix scipy build issue. · 7f6056dc
  Blaise Li authored Dec 18, 2019
  
  7f6056dc
17 Dec, 2019 1 commit
- Mounting thing necessary for multiprocessing. · 1e37c6ef
  Blaise Li authored Dec 17, 2019
```
Also remove niceload.
```
  1e37c6ef
13 Dec, 2019 1 commit
- Updating libhts to fix PyBigWig issue. · 5ae1c42f
  Blaise Li authored Dec 13, 2019
  
  5ae1c42f
09 Dec, 2019 2 commits
- Using more processors to map and index. · aaf097a4
  Blaise Li authored Dec 09, 2019
```
Hopefully this will be more efficient on pisa.
```
  aaf097a4
- Trying to relax memory limitations. · 2c544b0a
  Blaise Li authored Dec 09, 2019
```
Pisa has more memory. Trim and dedup seems to be a bottleneck.
```
  2c544b0a
20 Nov, 2019 1 commit
- Fix makefile. Symbolic link update was wrong. · 0906153c
  Blaise Li authored Nov 20, 2019
  
  0906153c
19 Nov, 2019 2 commits
- Merge branch 'master' of gitlab.pasteur.fr:bli/bioinfo_utils · 8ddf5ca7
  Blaise Li authored Nov 19, 2019
  
  8ddf5ca7
- Missing target og a link. · fc2f3556
  Blaise Li authored Nov 19, 2019
  
  fc2f3556
18 Nov, 2019 4 commits
- Missing R script. · e97f55e8
  Blaise Li authored Nov 18, 2019
  
  e97f55e8
- Added symlink to install step. · d55ce316
  Blaise Li authored Nov 18, 2019
  
  d55ce316
- Added and reorganized trimming scripts. · 964ae912
  Blaise Li authored Nov 18, 2019
  
  964ae912
- Add install rule in Makefile. · 9a0d87a3
  Blaise Li authored Nov 18, 2019
  
  9a0d87a3
14 Nov, 2019 2 commits
- Merge branch 'master' of gitlab.pasteur.fr:bli/bioinfo_utils · cfdaca57
  Blaise Li authored Nov 14, 2019
  
  cfdaca57
- Hide some HTS data files in .gitignore. · 94a9a806
  Blaise Li authored Nov 14, 2019
  
  94a9a806
05 Nov, 2019 1 commit
- Explaning how to build and use the container. · b1c06d55
  Blaise Li authored Nov 05, 2019
  
  b1c06d55
04 Nov, 2019 4 commits
- Tracking newer libhts. · 0c337568
  Blaise Li authored Nov 04, 2019
  
  0c337568
- Fix syntax error and variable name. · 2a04a039
  Blaise Li authored Nov 04, 2019
  
  2a04a039
- Error message may change? · 430fe610
  Blaise Li authored Nov 04, 2019
  
  430fe610
- Workaround check added in pyBigWig. · a26939b3
  Blaise Li authored Nov 04, 2019
```
See https://github.com/deeptools/pyBigWig/issues/97
```
  a26939b3
30 Oct, 2019 6 commits
- Trying to use libreads for id conversions. · f6ff4000
  Blaise Li authored Oct 30, 2019
  
  f6ff4000
- Reverting snakefiles to use plain wrappers_dir. · e10a0af2
  Blaise Li authored Oct 30, 2019
  
  e10a0af2
- Merge branch 'master' of gitlab.pasteur.fr:bli/bioinfo_utils · 182bef09
  Blaise Li authored Oct 30, 2019
  
  182bef09
- Fix path to snakemake wrappers. · 233cb758
  Blaise Li authored Oct 30, 2019
  
  233cb758
- Fix path to snakemake wrappers. · 0eb879a8
  Blaise Li authored Oct 30, 2019
  
  0eb879a8
- Singularity definition and wrappers. · 0f0690f0
  Blaise Li authored Oct 30, 2019
  
  0f0690f0
29 Oct, 2019 5 commits
- Missing parser for BeautifulSoup. · 3f5db2cd
  Blaise Li authored Oct 29, 2019
  
  3f5db2cd
- Follow new version of libhts. · 7aadfa00
  Blaise Li authored Oct 29, 2019
  
  7aadfa00
- Homegenize ghc version, fix link. · dc403893
  Blaise Li authored Oct 29, 2019
  
  dc403893
- Missing update. · 1d9cb4f8
  Blaise Li authored Oct 29, 2019
  
  1d9cb4f8
- Update submodules. · bfbc3c7e
  Blaise Li authored Oct 29, 2019
  
  bfbc3c7e
28 Oct, 2019 8 commits
- Packaging snakemake wrappers. · 4d011079
  Blaise Li authored Oct 28, 2019
  
  4d011079
- Still updating snakemake_wrapper. · be88479c
  Blaise Li authored Oct 28, 2019
  
  be88479c
- Missing file for the Haskell T-tail trimmer. · dd1cbfd6
  Blaise Li authored Oct 28, 2019
  
  dd1cbfd6
- Added missing Haskell program. · ffa792b8
  Blaise Li authored Oct 28, 2019
  
  ffa792b8
- Record deploy token for libreads. · a1cd92a6
  Blaise Li authored Oct 28, 2019
  
  a1cd92a6
- Track newer snakemake_wrappers · a11703b9
  Blaise Li authored Oct 28, 2019
  
  a11703b9
- More requirements specified. Missing dir link. · 30730e63
  Blaise Li authored Oct 28, 2019
  
  30730e63
- Typo in requirements. · 91c34cd9
  Blaise Li authored Oct 28, 2019
  
  91c34cd9
21 Oct, 2019 2 commits
- Requirements for some workflows. · 4b38e5c1
  Blaise Li authored Oct 21, 2019
  
  4b38e5c1
- Updating submodules, deploy tokens. · af8998bf
  Blaise Li authored Oct 21, 2019
  
  af8998bf