chapmanb/cloudbiolinux

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Sep 3, 2013 Add support for MacOX Homebrew (and Linuxbrew port) package manager. …
	1	# Packages available in the Homebrew and Linuxbrew package manager
	2	---
	3	bio_nextgen:
	4	alignment:
Oct 31, 2013 Re-enable additional brew-based builds with --env=inherit set thanks …
	5	- bwa
Sep 3, 2013 Add support for MacOX Homebrew (and Linuxbrew port) package manager. …
	6	- bowtie2
	7	- novoalign
Feb 26, 2014 Move to homebrew package for RNA-seq STAR aligner
	8	- rna-star
Sep 3, 2013 Add support for MacOX Homebrew (and Linuxbrew port) package manager. …
	9	utilities:
Oct 31, 2013 Re-enable additional brew-based builds with --env=inherit set thanks …
	10	- bamtools
Sep 3, 2013 Add support for MacOX Homebrew (and Linuxbrew port) package manager. …
	11	- bedtools
Apr 4, 2014 Add cramtools and rtg-tools support through brew installs. Remove old…
	12	- cramtools
Mar 15, 2014 Move biobambam and libmaus build to brew packages instead of custom b…
	13	- biobambam
Sep 3, 2013 Add support for MacOX Homebrew (and Linuxbrew port) package manager. …
	14	- fastqc
Dec 2, 2013 Add fastx_toolkit as homebrew dependency instead of custom build. Inc…
	15	- fastx_toolkit
Oct 22, 2013 Enable homebrew/linuxbrew integration as part of default CloudBioLinu…
	16	- qualimap
Nov 28, 2014 Avoid brew conflicts with new build-only upstream version of sambamba…
	17	- sambamba-binary
Apr 4, 2014 Include Staden io_lib with support for CRAM indexing and retrieval by…
	18	- staden_io_lib
Sep 3, 2013 Add support for MacOX Homebrew (and Linuxbrew port) package manager. …
	19	analysis:
Dec 11, 2014 Update cufflinks to point to new binary locations. Use homebrew binar…
	20	- cufflinks-binary
Sep 24, 2014 samtools 1.x is now the default in homebrew, skip looking for --devel…
	21	- samtools
May 19, 2014 Remove separate tabix install since tabix now included in bcftools as…
	22	- htslib
	23	- bcftools
Sep 3, 2013 Add support for MacOX Homebrew (and Linuxbrew port) package manager. …
	24	#- tophat
	25	variant:
Aug 9, 2014 Add delly structural variant caller with binary install. Enable passi…
	26	- delly;--with-binary
Feb 23, 2014 Move FreeBayes build to use brew recipe. Add Platypus caller
	27	- freebayes
Sep 19, 2014 Add pindel and non-head seqtk to current bcbio packages
	28	- gatk-framework
Jan 21, 2015 Add lofreq brew package
	29	- lofreq
Oct 31, 2013 Re-enable additional brew-based builds with --env=inherit set thanks …
	30	- lumpy-sv
Sep 19, 2014 Add pindel and non-head seqtk to current bcbio packages
	31	- pindel
Feb 23, 2014 Fix platypus brew target to avoid naming collision
	32	- platypus-variant
Apr 4, 2014 Add cramtools and rtg-tools support through brew installs. Remove old…
	33	- rtg-tools
Sep 19, 2014 Add pindel and non-head seqtk to current bcbio packages
	34	- scalpel
Jun 3, 2014 Update to latest version of snpEff, GEMINI and VEP. Prefer brew insta…
	35	- snpeff
Oct 24, 2014 Add homebrew recipes for THetA2 and WHAM to default builds for bcbio …
	36	- theta2
Jul 23, 2014 Add vardict as default install target for bcbio. (chapmanb/bcbio-next…
	37	- vardict
Dec 5, 2013 Add homebrew versions of vcflib and glia packages, and make available…
	38	- vcflib
Oct 22, 2013 Enable homebrew/linuxbrew integration as part of default CloudBioLinu…
	39	- vcftools
Jun 3, 2014 Update to latest version of snpEff, GEMINI and VEP. Prefer brew insta…
	40	- vep
Oct 24, 2014 Add homebrew recipes for THetA2 and WHAM to default builds for bcbio …
	41	- wham
Dec 22, 2014 Yaha does not download at the moment.
	42	# - yaha The Principal Investigator has moved; the software does not download ATM
Aug 7, 2015 Packages for metasv support + Biointerchange
	43	integration:
	44	- biointerchange
Nov 1, 2013 Remove custom GNU parallel custom target, replacing with brew GNU par…
	45	distributed:
Sep 8, 2014 Move to samtools 1.0, support brew version checking on devel versions
	46	- parallel