Commits · 00b599a0140f4e756f0e2132e3e26560a3feb5b6 · SOaAS / psot.repository · GitLab

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Feb 12, 2019
- add "docker" AND "singularity" properties in module configs; config.py reads... · 00b599a0
  Marc authored 6 years ago
  
  add "docker" AND "singularity" properties in module configs; config.py reads named options correctly
  00b599a0
- add "docker" and "singularity" programm arguments to psot; extend scripts and... · 9c99ece0
  Marc authored 6 years ago
  
  add "docker" and "singularity" programm arguments to psot; extend scripts and config files for blastp, ghostx and hmmer
  9c99ece0
Feb 10, 2019
- default_repo is now loaded as default repository at programm start · c344cdf1
  Marc authored 6 years ago
  
  c344cdf1
- bug fixed: nextflow.config now also correct if processes are not started in virtual environment · d222fc30
  Marc authored 6 years ago
  
  d222fc30
Feb 09, 2019
- include 'executor', 'clusterOptions' and 'beforeScript' properties in nextflow.config generation · 08bdbb12
  Marc authored 6 years ago
  
  08bdbb12
- run scripts can now "look up" if they were started inside of the container · e7854eff
  Marc authored 6 years ago
  
  e7854eff
Feb 08, 2019
- netxflow.py generates a nextflow.config file now; add container element in... · 4d48a8a1
  Marc authored 6 years ago
  
  netxflow.py generates a nextflow.config file now; add container element in some modules in the default_repo
  4d48a8a1
Apr 09, 2018
- Fix bug: information cannot be retrieved when no computations are available · a736ef30
  Lukas Jelonek authored 6 years ago
  
  a736ef30
Apr 04, 2018
- Fix bug: Exception when no repository is available · 0c33a710
  Lukas Jelonek authored 6 years ago
  
  0c33a710
Apr 03, 2018
- Fix bug: tools is not a dictionary when not defined in config.yaml · 2e5f8186
  Lukas Jelonek authored 6 years ago
  
  2e5f8186
- Remove commandline parameter for additional repositories · b3f128d5
  Lukas Jelonek authored 6 years ago
  
  b3f128d5
- Decouple default bcf psot profiles from psot · c1aafe51
  Lukas Jelonek authored 6 years ago
  
  c1aafe51
- Move repository parameter to main parser. Improve debug output · 158711ed
  Lukas Jelonek authored 6 years ago
  
  158711ed
Mar 08, 2018
- Add envelop to hmmer output, replace blast with ghostx in common profile · 7429e324
  Lukas Jelonek authored 7 years ago
  
  7429e324
Mar 07, 2018
- Fix bug: hmmer query start and end are same or similar · 3d4c8474
  Lukas Jelonek authored 7 years ago
  
  3d4c8474
- Fix bug: convert_targetp still has problems when installed in a virtualenv · 0ef7a504
  Lukas Jelonek authored 7 years ago
  
  0ef7a504
- Fix bug: Cluster execution does not work within a virtual environment · 8c34e904
  Lukas Jelonek authored 7 years ago
  
  8c34e904
Feb 07, 2018
- Implement support for accessing modules from other repositories in profiles · 8b448cb6
  Lukas Jelonek authored 7 years ago
  
  8b448cb6
- Fix bug: adapt targetp runner to new helpers path · 0a11c872
  Lukas Jelonek authored 7 years ago
  
  0a11c872
- Fix bug: adapt ghostx runner to new helpers path · 4f316a5c
  Lukas Jelonek authored 7 years ago
  
  4f316a5c
- Moved helper scripts to own directory. Use absolute paths for scripts. · 78d90258
  Lukas Jelonek authored 7 years ago
  
  78d90258
Jan 31, 2018
- Add user interface integration for psot repositories via cli and environment variable · 67704550
  Lukas Jelonek authored 7 years ago
  
  67704550
- Fix bug: retrieve information uses always the same name (fixes #45) · a7249505
  Lukas Jelonek authored 7 years ago
  
  a7249505
- Implement merge of multiple psot repositories · 278b28bc
  Lukas Jelonek authored 7 years ago
  
  278b28bc
- Replace uuid in live results with tool name (resolves #20). · 044a1df9
  hmueller authored 7 years ago
  
  044a1df9
Jan 30, 2018
- Add test methods for checking whether scripts for repository are resolved correctly. · c62b52a7
  Lukas Jelonek authored 7 years ago
  
  c62b52a7
- Refactor config into repository and application config. · 6cfc2cf4
  Lukas Jelonek authored 7 years ago
  
  6cfc2cf4
Jan 29, 2018
- Fix bug: replace default fasta file with concrete fasta file · c5e97033
  Lukas Jelonek authored 7 years ago
  
  c5e97033
Jan 24, 2018
- Add feature: dbxref lookup (closes #23) · dad7e862
  Lukas Jelonek authored 7 years ago
  
  Sem-Ver: feature
  dad7e862
- Replace single document handling with dictionary documents handling for dbxref resolver · a0fdafcd
  Lukas Jelonek authored 7 years ago
  
  a0fdafcd
- Add script to resolve dbxrefs for psot results · 3b7d874f
  Lukas Jelonek authored 7 years ago
  
  3b7d874f
- Fix bug: Analysis is executed even if no valid file is given (fixes #39) · 7ecd0ccd
  Lukas Jelonek authored 7 years ago
  
  Sem-Ver: bugfix
  7ecd0ccd
- Fix bug: TMHMM json output result key should hold a list (solves #32) · 60e4da60
  Lukas Jelonek authored 7 years ago
  
  Sem-Ver: bugfix
  60e4da60
- Add setup script. Move all resources to psot module · d32426b0
  Lukas Jelonek authored 7 years ago
  
  d32426b0
Dec 12, 2017
- added resolve_dbxrefs.py to nextflow.py (not working yet) · 458a3c11
  lmueller authored 7 years ago
  
  458a3c11
Nov 21, 2017
- Replace drmaa with SGE · 301d74c2
  Lukas Jelonek authored 7 years ago
  
  301d74c2
Aug 10, 2017
- Set java drmaa lib before running nextflow · ecf65900
  Lukas Jelonek authored 7 years ago
  
  ecf65900
- Add --use_cluster flag to CLI and pass it to the nextflow executor · 13a05b98
  Lukas Jelonek authored 7 years ago
  
  13a05b98
- Set /vol/sge-tmp as temporary folder · 7aeb1be9
  Lukas Jelonek authored 7 years ago
  
  7aeb1be9
- Add chunkprocessing via drmaa · 6dbf885c
  Lukas Jelonek authored 7 years ago
  
  6dbf885c