Code

Cytoscape#66

Code

Merged

agitter merged 49 commits intomasterReed-CompBio/spras:masterfrom cytoscapeReed-CompBio/spras:cytoscapeCopy head branch name to clipboardSep 22, 2023

+386-43

Commits

Commits on Apr 25, 2022

• add cytoscape post processing

  ajshedivy

  committed
  8600f45

Commits on Jun 27, 2022

• add py4cytoscape container and dev stuff

  ajshedivy

  committed
  da5a00f

Commits on Jun 28, 2022

• integrate cytoscape into snakemake

  ajshedivy

  committed
  635c6ed

Commits on Jun 29, 2022

• remove py4cy package

  ajshedivy

  committed
  ca5ab35

• add cytoscape to config.yaml

  ajshedivy

  committed
  5b6567c

Commits on Jul 5, 2022

• code review changes

  ajshedivy

  committed
  e464451

• add other changes

  ajshedivy

  committed
  3739a9a

Commits on Jul 6, 2022

• Merge branch 'master' into cytoscape

  agitter

  authored
  60816a5

Commits on Jul 9, 2022

• Check whether tests pass with Cytoscape step disabled

  agitter

  committed
  d6521b5

• Whitespace formatting

  agitter

  committed
  3d03cec

• Remove prints

  agitter

  committed
  4816c0b

• Re-enable Cytoscape step

  agitter

  committed
  97e3c55

Commits on Aug 12, 2022

• Merge branch 'master' into cytoscape

  agitter

  authored
  1652f45

Commits on Aug 25, 2022

• Cleanup snakefile and init file

  agitter

  committed
  bdce7f8

• Move Cytoscape code

  agitter

  committed
  c26e19f

• Clean up Cytoscape util and Dockerfile

  Show description for 9635ad6
  agitter

  committed
  9635ad6

• Revert util changes

  agitter

  committed
  86702ac

• Switch Cytoscape wrapper to use generic util

  Show description for 713466a
  agitter

  committed
  713466a

• Move Docker image to reedcompbio

  agitter

  committed
  3566390

Commits on Aug 26, 2022

• Allow file paths and pathway labels as arguments

  agitter

  committed
  79d5825

• Add Cytoscape Docker image build to workflow

  agitter

  committed
  4d1f3e0

• Implement Singularity support for Cytoscape

  agitter

  committed
  075013e

Commits on May 3, 2023

• Fix merge conflicts

  agitter

  committed
  d66ca3c

Commits on May 27, 2023

• Add initial readme

  agitter

  committed
  0439541

• Update Cytoscape for tab delimited pathways

  agitter

  committed
  ad71a8d

• Simplify Cytoscape connection by removing x11 and novnc

  agitter

  committed
  d9553e4

Commits on May 28, 2023

• Remove dependence on root inside image

  agitter

  committed
  92d53fa

• Remove unused auth file

  agitter

  committed
  f139e4b

Commits on Jun 10, 2023

• Create vmoptions and add to Docker image

  Show description for fdab0d7
  agitter

  committed
  fdab0d7

• Fix line endings and change memory usage

  agitter

  committed
  47ce1f1

Commits on Jun 22, 2023

• Update TODOs in readme

  agitter

  committed
  c2150a6

• Merge with master

  agitter

  committed
  b4a4def

• Run auto formatter

  agitter

  committed
  72580c9

Commits on Aug 25, 2023

• Merge branch 'master' into cytoscape

  agitter

  authored
  ec81f28

Commits on Sep 1, 2023

• Set HOME in Dockerfile

  Show description for 694b0f9
  agitter

  committed
  694b0f9

Commits on Sep 2, 2023

• Add Cytoscape zip error and alternative HOME workarounds

  Show description for 1d32311
  agitter

  committed
  1d32311

• Support Singularity HOME environment variable

  agitter

  committed
  d894c46

Commits on Sep 8, 2023

• Set up Cytoscape config file volume mapping

  agitter

  committed
  bd6c7d7

• Write one Cytoscape session per dataset

  agitter

  committed
  fa8a8e5

Commits on Sep 14, 2023

• Container now works in Singularity

  agitter

  authored
  c3fa558

Commits on Sep 15, 2023

• Rename and document Cytoscape function

  agitter

  committed
  cfc85ca

• Add Cytoscape test

  agitter

  committed
  62edad1

• Misc cleanup

  agitter

  committed
  344e1e7

Commits on Sep 16, 2023

• Add max connection retries

  agitter

  committed
  3c5e238

Commits on Sep 21, 2023

• Match Apptainer version to version on test server

  agitter

  committed
  4508c43

• Mark test expected to fail

  agitter

  committed
  fedc826

Commits on Sep 22, 2023

• Add v1 tag to Cytoscape image

  agitter

  committed
  ddc5b94

• Remove file with bad line endings

  agitter

  committed
  9622918

• Add back vmoptions file

  agitter

  committed
  80e70df