HPC:bcl2fastq

From HPC wiki

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, bcl2fastq2-v2.17.1.14. v2.19.0.316 and v2.20.0.422

Usage

Any of bcl2fastq2 can be loaded as a module:

[asrini@node61 ~]$ module avail

--------------------------------------------------------------------------------- /usr/share/Modules/modulefiles ----------------------------------------------------------------------------------
AllPaths-LG-v49967              bwa-0.7.10                      homer-v4.6                      pcre-8.38                       R/3.4.3                         sratoolkit-2.4.2
autoconf-2.69                   bzip2-1.0.6                     java-sdk-1.6.0                  perl5lib                        R-3.1.1                         STAR-2.3.0e
automake-1.15                   CASAVA-v1.8.2                   java-sdk-1.7.0                  picard-1.96                     R-3.1.2                         STAR-2.4.1d
bamtools-2.3.0                  CGAL-4.7                        java-sdk-1.8.0                  picard-tools-1.141              R-3.2.1                         STAR-2.5.2a
bcl2fastq2/v2.15.0.4            circos-0.67-5                   kClust-1.0                      pkg-config-path                 R-3.2.2                         STAR-hg19
bcl2fastq2/v2.16.0.10           cufflinks-2.2.0                 ld-library-path                 plink-1.90b3b                   R-3.3.0                         STAR-mm9
bcl2fastq2/v2.17.1.14           cufflinks-2.2.1                 libtool-2.4.6                   python-2.7.5                    R-3.3.1                         texinfo-6.0
bcl2fastq2/v2.19.0.316          curl-7.49.0                     local_coreutils-8.24            python-2.7.9                    r-libs-user                     texlive-20170214
bcl2fastq2/v2.20.0.422          devtoolset-2                    manpath                         python-3.4.2                    ruby-1.9.3-p551                 tophat-2.0.11
bcl2fastq2-v2.15.0.4            dot                             module-git                      python-3.6.3                    ruby-2.1.5                      Trimmomatic-0.32
bcl2fastq2-v2.16.0.10           EMBOSS-6.6.0                    module-info                     qiime-1.8.0                     rum-2.0.5_05                    trinity-r20140717
bcl2fastq2-v2.17.1.14           eQtlBma-1.2.2                   modules                         R/3.1.1                         rum-2.0.5_06                    use.own
bcl2fastq2-v2.19.0.316          eQtlBma-1.3.1                   NAMD-2.9-Linux-x86_64-multicore R/3.1.2                         sailfish-0.6.3                  WiggleTools-1.0
blat-v35                        FastQC-0.11.2                   ncbi-blast-2.2.0                R/3.2.1                         samtools-0.1.18                 xz-5.2.2
boost-1.55.0                    fastx_toolkit-0.0.14            ngsutils-0.5.7                  R/3.2.2                         samtools-0.1.19                 zlib-1.2.8-1
boost-1.57.0                    gcc/5.3.1                       null                            R/3.3.0                         samtools-1.1
bowtie2/2.3.4.1                 gcc/6.2.1                       openmpi-1.5.4-x86_64            R/3.3.1                         scons-2.3.1-1
bowtie2-2.1.0                   gsl-2.1                         pandoc/2.0.6                    R/3.4.2                         SOAPdenovo2-r240

---------------------------------------------------------------------------------------- /etc/modulefiles -----------------------------------------------------------------------------------------
mpich-x86_64   openmpi-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.

Note the difference in module usage:

[asrini@node062 ~]$ module load bcl2fastq2/v2.20.0.422 

[asrini@node062 ~]$ bcl2fastq --version
BCL to FASTQ file converter
bcl2fastq v2.20.0.422
Copyright (c) 2007-2017 Illumina, Inc.



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