BioBuilds 2015.11

BioBuilds 2015.11 is the second major release in 2015. The most significant change in this release has been the switch from tarballs to Miniconda as the installation mechanism. Please refer to the Downloads page and Release Notes for information about how to use this new installer.

This release contains upgrades (if available) for all previous packages, and adds 12 new packages for Linux and 16 new packages for OS X (several previously Linux-only packages have now been ported to OS X). In total, there are ~49 application packages in this release, not counting various support libraries and dependent packages (e.g., individual R packages contributing to the BioConductor packages):

Application Version New/Upgrade status
ALLPATHS-LG 52488 Upgrade (Linux only)
BAMtools 2.4.0 New
Barracuda 0.7.107b New (Linux only)
bedtools 2.25.0 Upgrade
Bfast 0.7.0a No change
Bioconductor 3.2 Upgrade
BioPython 1.66 New
Boost 1.54.0 No change
Bowtie 1.1.2 Upgrade
Bowtie2 2.2.6 Upgrade
BWA 0.7.12 Upgrade
ClustalW 2.1 New
Cufflinks 2.2.1 No change
EBSEQ (R) 1.10.0 New
EMBOSS 6.5.7 New
FASTA 36.3.8b Upgrade
FastQC 0.11.4 Upgrade
gnuplot 5.0.0 New
Graphviz 2.38.0 No change
HMMER 3.1b2 Upgrade
HTSeq 0.6.1 No change
htslib 1.2.1 No change
IGV 2.3.65 Upgrade
iSAAC 15.04.01 Upgrade (Linux only)
Matplotlib 1.5.0 New
Mothur 1.36.1 Upgrade
NCBI BLAST+ 2.2.31 Upgrade (New on OS X)
Numpy 1.9.2 Upgrade
Oases 0.2.8 New
Picard 1.140 Upgrade
PLINK 1.07 No change
Pysam 0.8.3 New
Python 2.7.10 Upgrade
R 3.2.2 Upgrade
RSEM 1.2.25 New
Samtools 1.2.0 Upgrade
SHRiMP 2.2.3 No change (New on OS X)
SOAP3-DP r177 No change (Linux only)
SOAPaligner 2.20 No change
SOAPbuilder 2.20 No change
SOAPdenovo2 2.4.240 No change (New on OS X)
SQLite 3.8.4.1 No change
STAR 2.4.2a Upgrade (New on OS X)
tabix 1.2.1 Upgrade
TMAP 3.4.0 No change
TopHat 2.1.0 Upgrade
Trinity 2.1.1 Upgrade (New on OS X)
variant_tools 2.6.3 New
Velvet 1.2.10 No change

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