BioBuilds 2017.11

BioBuilds 2017.11 is the second major release of 2017. This release uses the conda package manager and builds on the 2017.05 release by adding 12 packages and updating 22 existing ones. Please refer to the “Applications in BioBuilds 2017.11” table below for more details.

This release includes the “biobuilds-opt” package for Linux on x86_64 and Linux on POWER originally introduced in the 2017.05 release. This package adds the “opt” feature into your BioBuilds conda environment, which then causes the conda package manager to preferentially install “alternative” builds of selected built using the hardware vendor’s development toolchain (Intel Parallel Studio XE for x86_64 and IBM Advance Toolchain 10.0 for POWER). In most cases, such builds provide better performance than their counterparts built using the standard gcc-based toolchain.

This release also marks the start of our migration to building packages using the Anaconda 5 toolchains rather than OS-supplied ones. This switch lets us make use of newer compiler capabilities, particularly with regards to performance and security, while keeping support for older operating systems (e.g., CentOS/RedHat 6). It also allows us to reduce the need on external (i.e., OS-provided) dependencies, such as X11 shared libraries.

After installing conda, you can install BioBuilds 2017.11 by running:

conda update -c conda -y conda
conda create -c biobuilds -p /path/to/biobuilds-2017.11 biobuilds=2017.11 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-2017.11 biobuilds=2017.11

Adding “/path/to/biobuilds-2017.11/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 2017.11 Release Notes” for additional information about other installation options (including partial installs) and required system libraries.

Application Version Changes since 2017.05
20/20+ 1.1.3 New
ABySS 2.0.2 No change
ALLPATHS-LG 52488 No change (Linux only)
ARAGORN 1.2.38 No change
bamkit 16.07.26 No change
BAMstats 1.25 New
BAMtools 2.4.1 No change
Barracuda 0.7.107e No change (Linux only)
bcftools 1.6.0 Upgrade
BEAST 2.4.6 No change
bedops 2.4.26 No change
bedtools 2.26.0 No change
Bfast 0.7.0a No change
Bioconductor 3.6 Upgrade
BioPerl 1.6.924 No change
BioPython 1.70 Upgrade
Boost 1.62.0 No change
Bowtie 1.1.2 No change
Bowtie2 2.3.1 No change
BreakDancer 1.4.5 No change
BWA 0.7.17 Upgrade
Canu 1.5 No change
cgpVcf 2.20 New
chimerascan 0.4.5a No change
CLARK 1.2.3.1 No change
Clustal Omega 1.2.4 No change
ClustalW 2.1 No change
conifer 0.2.2 No change
Cufflinks 2.2.1 No change
cutadapt 1.13 No change
DELLY2 0.7.6 No change
DIAMOND 0.8.24 No change
drFAST 1.0.0.0 No change
EBSEQ (Bioconductor) 1.18.0 Upgrade
EMBOSS 6.6.0 No change
FASTA 36.3.8e No change
FASTQC 0.11.5 No change
FASTX-Toolkit 0.0.14 No change
FreeBayes 1.1.0 No change
GCTA 1.26.0 No change
GenomonFisher 0.2.0 No change
gnuplot 5.2.2 Upgrade
HISAT2 2.0.5 No change
HMMER 3.1b2 No change
HTSeq 0.6.1 No change
htslib 1.6.0 Upgrade
IGV 2.3.93 No change
Infernal 1.1.2 No change
iSAAC 04.17.09.06 Upgrade
jellyfish 2.2.7 New
kallisto 0.43.1 New
kmergenie 1.7044 New
Kraken 0.10.5_beta No change
Lighter 1.1.1 No change
LoFreq* 2.1.2 No change
LUMPY-SV 0.2.13 No change
Matplotlib 1.5.3 No change
migrate 3.6.11 New
Mothur 1.39.5 No change
MrBayes 3.2.6 No change
mrFAST 2.6.1.0 No change
mrsFAST 3.4.0 No change
MUSCLE 3.8.31 No change
NCBI BLAST+ 2.6.0 No change
NovelSeq 1.0.2 No change
NumPy 1.13.3 Upgrade
Oases 0.2.8 No change
OpenBLAS 0.2.20 Upgrade
Pandas 0.21.0 Upgrade
parallel 20160922 No change
Parasight 7.6 No change
Perl 5.22.0 No change
PHYLIP 3.696 No change
Picard 2.15.0 Upgrade
Pindel 0.2.5b8 No change
PLINK 1.07 No change
PLINK-NG 1.90b3.42 No change
Primer3 2.3.7 No change
Probabilistic 20/20 1.2.0 New
Prodigal 2.6.3 No change
Prokka 1.12 No change
Pysam 0.8.4 No change
Python 2.7.13 No change
R 3.4.2 Upgrade
R cowplot 0.9.1 Upgrade
R ggplot2 2.2.1 Upgrade
R rio 0.5.5 New
R sequenza 2.1.2 New
R tidyverse 1.2.1 Upgrade
RAxML 8.2.9 No change
RSEM 1.3.0 No change
Sailfish 0.10.0 No change
Salmon 0.7.2 No change
Sambamba 0.6.6 No change
SAMBLASTER 0.1.24 No change
Samtools 1.6.0 Upgrade
scalpel 0.5.3 No change
scikit-bio 0.4.2 No change
scikit-learn 0.19.1 New
SciPy 1.0.0 Upgrade
Seqtk 1.2.94 No change
SGA 0.10.15 New
SHRiMP 2.2.3 No change
SNAP 1.0beta.18 No change
Snippy 3.0 No change
SnpEff 4.3t Upgrade
SnpSift 4.3t 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 3.10.1 No change
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 No change
tabix 1.6.0 Upgrade
tassel 5.2.37 No change
tbl2asn 25.3 No change
TMAP 3.4.0 No change
TopHat 2.1.1 No change
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 No change
vcftools 0.1.15 Upgrade
Velvet 1.2.10 No change

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