BioBuilds 2016.11

BioBuilds 2016.11 is the second major release of 2016. This release continues to use Continuum Analytics’ (mini)conda installer and builds on the 2016.04 release by adding 19 packages and updating 36 existing ones. Please refer to the “Applications in BioBuilds 2016.11” table below for more details.

After installing conda, you can install BioBuilds 2016.11 by running:

conda update -c conda -y conda
conda config --set allow_softlinks false  # (optional; see below)
conda create -c biobuilds -p /path/to/biobuilds-2016.11 biobuilds=2016.11

Note that the “conda config --set allow_softlinks false” is optional, but can help prevent certain types of bugs in cases where BioBuilds and conda are installed on different file systems (UNIX mount points).

Adding “/path/to/biobuilds-2016.11/bin” to your $PATH environment variable (for example, by setting it in your ~/.bash_profile) will then allow you to run BioBuilds applications without providing a full path. Please refer to the “BioBuilds 2016.11 Release Notes” for additional information about other installation options (including partial installs) and required system libraries.

Applications in BioBuilds 2016.11

Application Version Changes since 2016.04
ALLPATHS-LG 52488 No change (Linux only)
bamkit 16.07.26 New
BAMtools 2.4.0 No change
Barracuda 0.7.107e No change (Linux only)
bcftools 1.3.1 Upgrade
bedops 2.4.20 New
bedtools 2.26.0 Upgrade
Bfast 0.7.0a No change
Bioconductor 3.4 Upgrade
BioPerl 1.6.924 No change
BioPython 1.68 Upgrade
Boost 1.62.0 Upgrade
Bowtie 1.1.2 No change
Bowtie2 2.2.9 Upgrade
BreakDancer 1.4.5 No change
BWA 0.7.15 Upgrade
chimerascan 0.4.5a No change
ClustalW 2.1 No change
conda >= 4.2.12 Upgraded, as needed
Cufflinks 2.2.1 No change
cutadapt 1.11 New
DELLY2 0.7.6 Upgrade
DIAMOND 0.8.24 New
EBSEQ (Bioconductor) 1.14.0 Upgrade
EMBOSS 6.6.0 Upgrade
FASTA 36.3.8e Upgrade
FASTQC 0.11.5 No change
FASTX-Toolkit 0.0.14 No change
FreeBayes 1.0.2 No change
GenomonFisher 0.2.0 Upgrade
gnuplot 5.0.5 Upgrade
Graphviz 2.38.0 No change
HMMER 3.1b2 No change
HTSeq 0.6.1 No change
htslib 1.3.2 Upgrade
IGV 2.3.88 Upgrade
iSAAC Upgrade (Linux only)
Kraken 0.10.5_beta New
LoFreq* 2.1.2 No change
LUMPY-SV 0.2.13 New
Matplotlib 1.5.3 Upgrade
Mothur 1.38.1 Upgrade
MrBayes 3.2.6 No change
MUSCLE 3.8.31 No change
NCBI BLAST+ 2.5.0 Upgrade
NumPy 1.11.2 Upgrade
Oases 0.2.8 No change
OpenBLAS 0.2.19 Upgrade
Pandas 0.19.1 Upgrade
parallel 20160922 New
Perl 5.22.0 No change
PHYLIP 3.696 No change
Picard 2.7.1 Upgrade
Pindel 0.2.5b8 No change
PLINK 1.07 No change
PLINK-NG 1.90b3.42 New
Primer3 2.3.7 New
Pysam 0.8.4 No change
Python 2.7.12 Upgrade
R 3.3.2 Upgrade
R cowplot 0.7.0 New
R tidyverse 1.0.0 New
RAxML 8.2.9 New
RSEM 1.3.0 Upgrade
Sailfish 0.10.0 Upgrade
Salmon 0.7.2 New
Samtools 1.3.1 Upgrade
scalpel 0.5.3 No change
scikit-bio 0.4.2 New
SciPy 0.18.1 Upgrade
Seqtk 1.2.94 New
SHRiMP 2.2.3 No change
SnpEff 4.3c Upgrade
SnpSift 4.3c Upgrade
SOAP3-DP r177 No change (Linux only)
SOAPaligner 2.20 No change
SOAPbuilder 2.20 No change
SOAPdenovo2 2.4.240 No change
SPAdes 3.9.0 New
SplazerS 1.3.3 No change
SQLite 3.13.0 Upgrade
SRA Tools >= 2.8.0 Upgraded, as needed
STAR 2.5.2b Upgrade
STAR-fusion 0.8.0 Upgrade
tabix 1.3.2 Upgrade
tassel 5.2.31 Upgrade
T-Coffee 11.00.8cbe486 No change
TMAP 3.4.0 No change
TopHat 2.1.1 No change
Trimmomatic 0.36 New
Trinity 2.2.0 No change
variant_tools 2.7.0 No change
vcftools 0.1.14 New
Velvet 1.2.10 No change

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