Commits

Commits on Mar 31, 2015

Avoid errors with multiple options to Python for ignoring environmental variables and local site-library #426
chapmanb
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59faa3b
Skip inclusion of local site-libraries when running GEMINI with -s flag. #426
chapmanb
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5ad343e
Avoid pulling in python libraries from a users local site library. Thanks to @bw2. #426
chapmanb
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abe91aa

Commits on Mar 28, 2015

Clean environmental variables PYTHONPATH/PYTHONHOME when doing installs and upgrades to prevent accidental library issues. Thanks to @brentp
chapmanb
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cf5340a

Commits on Mar 17, 2015

Commits on Mar 9, 2015

Avoid loading error for variants with missing ALT alleles. Fixes chapmanb/bcbio-nextgen#781
chapmanb
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2324887

Commits on Mar 8, 2015

Commits on Mar 6, 2015

Avoid extra newlines at end of tab delimited PED files. Fixes #386
chapmanb
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ded88df

Commits on Mar 4, 2015

Allow tab delimited PED files with whitespace in columns as input to GEMINI
chapmanb
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1618492

Commits on Mar 3, 2015

Set pip SSL certificates to point at installed conda SSL package if present. Avoids SSL errors when pip can't find system certificates. Thanks to Andrew Oler
chapmanb
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2b7c6c8

Commits on Feb 27, 2015

Enable gemini installs on 32-bit machines. Useful for supporting VirtualBox VMs
chapmanb
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00deb8c

Commits on Feb 25, 2015

Skip loading CADD annotations for variations with missing reference or alt genotypes. chapmanb/bcbio-nextgen#773
chapmanb
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566e1d7

Commits on Feb 24, 2015

Ensure openssl updated as part of gemini install/upgrade to avoid problems with older versions and SSL resolution
chapmanb
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1b78657

Commits on Feb 20, 2015

conda installation for ipython-cluster-helper and requirements like netifaces. Thanks to Gregory Putzel
chapmanb
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0a541ec

Commits on Feb 14, 2015

Make GEMINI install script back compatible to python 2.6 for Galaxy support. Fixes #378
chapmanb
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f3eee7e

Commits on Jan 13, 2015

Fix cyvcf version dependency for 0.11.0 release (fixes #363). Fix current gemini version in main requirements
chapmanb
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3216a9e

Commits on Nov 26, 2014

Correctly check for scheduler and queue options being present without requiring queue first in the argument list. Thanks to Andrew Oler
chapmanb
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c2ad9de

Commits on Nov 17, 2014

Use correct separator for LOFTEE human_ancestor file. Thanks to @drmjc. chapmanb/bcbio-nextgen#468
chapmanb
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4539d8c

Commits on Oct 31, 2014

Provide ability to update third party tools along with gemini itself
chapmanb
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1a9278c

Commits on Oct 3, 2014

Avoid picking up empty extra files for post-GEMINI annotation
chapmanb
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c6c1a4c

Commits on Sep 30, 2014

Work around issue in pysam when handling tabix inputs with large numbers of blank columns, which occurs when annotating with results from VEP: https://github.com/pysam-developers/pysam/pull/44
chapmanb
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a1a2008

Commits on Sep 18, 2014

Support for fitCons: indicator of potential for interesting function in genomic variants
chapmanb
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8d21d3d

Commits on Aug 15, 2014

Avoid using global gemini-config.yaml files when writing configuration to enable creation of multiple geminis on a single system #316
chapmanb
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b61891e

Commits on Jul 18, 2014

Commits on Jul 14, 2014

Update ez_setup to latest version to resolve issues with pypi mirrors: chapmanb/bcbio-nextgen#499
chapmanb
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d6dc9e1

Commits on Jun 27, 2014

Document loading of additional arbitrary VEP fields into GEMINI variants table
chapmanb
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81aa4e2

Commits on Jun 17, 2014

Provide automated annotation of extra fields in VEP file inputs. Additional fields are extracted, classified by type, formatted into a BED file and added to final GEMINI database using the standard…
chapmanb
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0fa4285

Commits on Jun 13, 2014

Include bcbio conda channel to provide up to date version of pysam (0.7.7) whih fixes a number of BAM parsing issues
chapmanb
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c6c5fd6