Releases · CGATOxford/cgat

25 May 08:31

Bugfixing release Latest

Latest

Fix GO.py for dumping ensembl annotations for versions > 88 ; #384 ; #385 ; #386
make sure we stick to conda 4.3 until a workaround is found for conda 4.4 ; #387
bed2bed.py: new method rename-chr ; #389
gff2gff.py: new method rename-chr ; #390
put test_import.py and test_style.py back ; #391
update conda from 4.3 to 4.5 (solving "CXXABI_1.3.9' not found" error ; ContinuumIO/anaconda-issues#5191) ; beffc47...abfe82b
added test for C/C++ compiler ; #394

Assets 2

18 Dec 15:51

Bugfixing release

Assets 2

17 Nov 11:21

Bugfixes for Python 3

bugfix cgat CLI
added scripts to help find R and Python dependencies: scripts/cgat_deps_R.sh, scripts/cgat_deps_python.sh
modified install script to use conda environment files instead of conda meta-packages; #343
update test_style.py to reflect new repository structure; #345
update test_import.py to reflect new repository structure; decc5ec
added script to perform Gene Set Enrichment Analysis; #344
updated scripts to work with Python 3.6; #346
bugfix bed2bed script; #349; #347
bugfix GTF.py module file; #350
various bugfixes for Python 3 problems when running pipeline_annotations in python 3, plus a modification of the new "assembly report" section to allow genomes without a standard assembly report (e.g. yeast) to be processed; #348
refactor CGAT/PipelineGWAS.py to CGAT/GWAS.py; #354
removed unused imports with autoflakes; #355
removed basestr, use str instead in Python 3; #359
added test for csv2db; #360
fixed rename_transcripts test for gtf2gtf.py; #361
updated installation; #364 ; #373
updated documentation; #365 ; #367
replaced bx.bbi.bigwig_file with pyBigWig ; #369
updated Expression.py to iterate over pandas dataframe; #370
updated Expression.py to work with DESeq2 > 1.16 ; #371
moved bed_vs_bed.py to obsolete ; #372