bcl2fastq
A few different versions of bcl2fastq2 are installed across all HPC nodes. The available versions are: bcl2fastq2-v2.15.0.4, bcl2fastq2-v2.16.0.10 and bcl2fastq2-v2.17.1.14.
Usage
Any of bcl2fastq2 can be loaded as a module:
[asrini@node61 ~]$ module avail --------------------------------------------------------- /usr/share/Modules/modulefiles --------------------------------------------------------- AllPaths-LG-v49967 EMBOSS-6.6.0 openmpi-1.5.4-x86_64 rum-2.0.5_06 autoconf-2.69 eQtlBma-1.2.2 pcre-8.38 sailfish-0.6.3 automake-1.15 eQtlBma-1.3.1 perl5lib samtools-0.1.18 bamtools-2.3.0 FastQC-0.11.2 picard-1.96 samtools-0.1.19 bcl2fastq2-v2.15.0.4 fastx_toolkit-0.0.14 picard-tools-1.141 samtools-1.1 bcl2fastq2-v2.16.0.10 gsl-2.1 pkg-config-path scons-2.3.1-1 bcl2fastq2-v2.17.1.14 homer-v4.6 plink-1.90b3b SOAPdenovo2-r240 blat-v35 java-sdk-1.6.0 python-2.7.5 sratoolkit-2.4.2 boost-1.55.0 java-sdk-1.7.0 python-2.7.9 STAR-2.3.0e boost-1.57.0 kClust-1.0 python-3.4.2 STAR-2.4.1d bowtie2-2.1.0 ld-library-path qiime-1.8.0 STAR-2.5.2a bwa-0.7.10 libtool-2.4.6 R-3.1.1 STAR-hg19 bzip2-1.0.6 local_coreutils-8.24 R-3.1.2 STAR-mm9 CASAVA-v1.8.2 manpath R-3.2.1 texinfo-6.0 CGAL-4.7 module-git R-3.2.2 tophat-2.0.11 circos-0.67-5 module-info R-3.3.0 Trimmomatic-0.32 cufflinks-2.2.0 modules R-3.3.1 trinity-r20140717 cufflinks-2.2.1 NAMD-2.9-Linux-x86_64-multicore r-libs-user use.own curl-7.49.0 ncbi-blast-2.2.0 ruby-1.9.3-p551 WiggleTools-1.0 devtoolset-2 ngsutils-0.5.7 ruby-2.1.5 xz-5.2.2 dot null rum-2.0.5_05 zlib-1.2.8-1 ---------------------------------------------------------------- /etc/modulefiles ---------------------------------------------------------------- mpich-x86_64 [asrini@node061 ~]$ module load bcl2fastq2-v2.17.1.14 [asrini@node061 ~]$ bcl2fastq --version BCL to FASTQ file converter bcl2fastq v2.17.1.14 Copyright (c) 2007-2015 Illumina, Inc.
