BioBuilds 2017.05

BioBuilds 2017.05 is the first major release of 2017. This release uses Continuum Analytics’ (mini)conda installer and builds on the 2016.11 release by adding 23 packages and updating 19 existing ones. Please refer to the “Applications in BioBuilds 2017.05” table below for more details.

This release also introduces the “biobuilds-opt” package for Linux on x86_64 and Linux on POWER, which installs the “opt” feature into your BioBuilds (conda) environment. This feature will preferentially install “alternative” versions of select tools built using the hardware vendor’s development toolchain (Intel Parallel Studio XE for x86_64 and IBM Advance Toolchain 10.0 for POWER), which in most cases, provide better performance than their counterparts built using the standard gcc-based toolchain.

After installing conda, you can install BioBuilds 2017.05 by running:

conda update -c conda -y conda
conda create -c biobuilds -p /path/to/biobuilds-2017.05 biobuilds=2017.05 biobuilds-opt

The above command will install the “opt”-enabled versions of various tools, if available. If, for some reason, you prefer _not_ to use “opt”-enabled tools, simply omit the “biobuilds-opt” package from the `conda create` command; i.e.,

conda create -c biobuilds -p /path/to/biobuilds-2017.05 biobuilds=2017.05

Adding “/path/to/biobuilds-2017.05/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 2017.05 Release Notes” for additional information about other installation options (including partial installs) and required system libraries.

Application Version Changes since 2016.11
ABySS 2.0.2 New
ALLPATHS-LG 52488 No change (Linux only)
ARAGORN 1.2.38 New
bamkit 16.07.26 No change
BAMtools 2.4.1 Upgrade
Barracuda 0.7.107e No change (Linux only)
bcftools 1.3.1 “opt”-enabled
BEAST 2.4.6 New
bedops 2.4.26 Upgrade
bedtools 2.26.0 “opt”-enabled
Bfast 0.7.0a “opt”-enabled
Bioconductor 3.4 No change
BioPerl 1.6.924 No change
BioPython 1.69 Upgrade
Boost 1.62.0 No change
Bowtie 1.1.2 No change
Bowtie2 2.3.1 Upgrade
BreakDancer 1.4.5 No change
BWA 0.7.15 “opt”-enabled
Canu 1.5 New
chimerascan 0.4.5a No change
CLARK 1.2.3.1 New
Clustal Omega 1.2.4 New
ClustalW 2.1 “opt”-enabled
conda >= 4.3.14 Upgraded, as needed
conifer 0.2.2 New
Cufflinks 2.2.1 No change
cutadapt 1.13 Upgrade
DELLY2 0.7.6 No change
DIAMOND 0.8.24 No change
drFAST 1.0.0.0 New
EBSEQ (Bioconductor) 1.14.0 No change
EMBOSS 6.6.0 No change
FASTA 36.3.8e “opt”-enabled
FASTQC 0.11.5 No change
FASTX-Toolkit 0.0.14 “opt”-enabled
FreeBayes 1.1.0 Upgrade
GCTA 1.26.0 New
GenomonFisher 0.2.0 No change
gnuplot 5.0.0 No change
Graphviz 2.38.0 No change
HISAT2 2.0.5 New
HMMER 3.1b2 No change
HTSeq 0.6.1 No change
htslib 1.3.2 “opt”-enabled
IGV 2.3.93 Upgrade
Infernal 1.1.2 New
iSAAC 03.16.09.21 No change (Linux only)
Kraken 0.10.5_beta “opt”-enabled
Lighter 1.1.1 New
LoFreq* 2.1.2 “opt”-enabled
LUMPY-SV 0.2.13 “opt”-enabled
Matplotlib 1.5.3 No change
Mothur 1.39.5 Upgrade
MrBayes 3.2.6 No change
mrFAST 2.6.1.0 New
mrsFAST 3.4.0 New
MUSCLE 3.8.31 “opt”-enabled
NCBI BLAST+ 2.6.0 Upgrade
NovelSeq 1.0.2 New
NumPy 1.12.1 Upgrade
Oases 0.2.8 “opt”-enabled
OpenBLAS 0.2.19 No change
Pandas 0.20.1 Upgrade
parallel 20160922 No change
Parasight 7.6 New (Linux only)
Perl 5.22.0 No change
PHYLIP 3.696 No change
Picard 2.9.2 Upgrade
Pindel 0.2.5b8 “opt”-enabled
PLINK 1.07 “opt”-enabled
PLINK-NG 1.90b3.42 No change
Primer3 2.3.7 “opt”-enabled
Prodigal 2.6.3 New
Prokka 1.12 New
Pysam 0.8.4 No change
Python 2.7.13 Upgrade
R 3.3.2 No change
R cowplot 0.7.0 No change
R tidyverse 1.0.0 No change
RAxML 8.2.9 No change
RSEM 1.3.0 “opt”-enabled
Sailfish 0.10.0 No change
Salmon 0.7.2 No change
Sambamba 0.6.6 New
SAMBLASTER 0.1.24 Upgrade
Samtools 1.3.1 “opt”-enabled
scalpel 0.5.3 “opt”-enabled
scikit-bio 0.4.2 No change
SciPy 0.19.0 Upgrade
Seqtk 1.2.94 “opt”-enabled
SHRiMP 2.2.3 “opt”-enabled
SNAP 1.0beta.18 New
Snippy 3.0 New
SnpEff 4.3o Upgrade
SnpSift 4.3o Upgrade
SOAP3-DP r177 No change (Linux only)
SOAPaligner 2.20 “opt”-enabled
SOAPbuilder 2.20 “opt”-enabled
SOAPdenovo2 2.4.240 “opt”-enabled
SPAdes 3.10.1 Upgrade
SplazerS 1.3.3 No change
SQLite 3.13.0 No change
SRA Tools >= 2.8.0 Upgraded, as needed
STAR 2.5.2b No change
STAR-fusion 0.8.0 No change
T-Coffee 11.00.8cbe486 “opt”-enabled
tabix 1.3.2 “opt”-enabled
tassel 5.2.37 Upgrade
tbl2asn 25.3 New
TMAP 3.4.0 “opt”-enabled
TopHat 2.1.1 “opt”-enabled
Trimmomatic 0.36 No change
Trinity 2.2.0 No change
variant_tools 2.7.0 No change
vcflib 1.0.0_rc1_16.05.18 New
vcftools 0.1.14 No change
Velvet 1.2.10 “opt”-enabled

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