BioBuilds 2015.04

BioBuilds 2015.04 is a major release that adds the following bioinformatics tools:

Tools Version Platforms Supported
IGV 2.3.49 x86_64 Linux*, x86_64 OS X*, POWER8 BE (RHEL)*, POWER8 LE (Ubuntu)*
iSAAC (Illumina aligner) 01.15.02.08 x86_64 Linux, POWER8 LE (Ubuntu)
TMAP (IonTorrent aligner) 3.4.0 x86_64 Linux, x86_64 OS X, POWER8 LE (Ubuntu)
RNAStar 2.4.0j x86_64 Linux, POWER8 BE (RHEL), POWER8 LE (Ubuntu)
SOAPaligner/soap2
(including soapbuilder)
2.20 x86_64 Linux, x86_64 OS X, POWER8 LE (Ubuntu)

* IGV for all platforms requires a Java runtime (JRE) be installed.

This release also provides access to a beta version of iRODS for little-endian POWER8 systems. Please refer to the “iRODS 4.1.0 for ppc64le” page for further details.

The following tools and libraries were updated:

Tools Version Platforms Supported
Bowtie2 2.2.4 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
BWA 0.7.12 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
OpenSSL 1.0.2a x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)

All other tools from previous releases are also included:

Tools Version Platforms Supported
ALLPATHS-LG 50960 x86_64 Linux*, POWER8 Linux (Ubuntu)
bedtools 2.21.0 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
bfast 0.7.0a x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
BioConductor Base 3.0 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
BLAST (NCBI) 2.2.29+ x86_64 Linux, POWER8 (RHEL), POWER8 (Ubuntu)
Bowtie 1.1.0 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
Cufflinks 2.2.1 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
FASTA 36.3.7a x86_64 Linux, POWER8 (RHEL), POWER8 (Ubuntu)
FastQC 0.11.2 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
HMMER 3.1b1 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
HTSeq 0.6.1 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
Mothur 1.33.3 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
numpy 1.9.0 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
PICARD 1.124 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
PLINK 1.07 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
Python 2.7.8 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
R 3.1.2 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
SAMTools 0.1.19 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
SAMTools 1.0 1.0 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
SHRiMP 2.2.3 x86_64 Linux, POWER8 (RHEL), POWER8 (Ubuntu)
SOAP3-DP 2.3.177 GPU-enabled Power8 (Ubuntu)
SOAPDenovo 2.4.0 x86_64 Linux, POWER8 (RHEL), POWER8 (Ubuntu)
SQLite 3.8.7.1 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
tabix 0.2.6 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
TopHat 2.0.13 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)
Trinity r20140717 x86_64 Linux**, POWER8 (Ubuntu)
Velvet/Oases 1.2.10 x86_64 Linux, x86_64 OS X, POWER8 (RHEL), POWER8 (Ubuntu)


* ALLPATHS-LG for x86_64 is not available for Ubuntu12.04 and CentOS6 due to compiler limitations.
** Trinity for x86_64 is currently not available for Ubuntu12.04 and CentOS6 due to compiler limitations.

BioBuilds 2015.04 can be downloaded here.

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