Difference between revisions of "HPC:bcl2fastq"
From HPC wiki
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=== bcl2fastq === | === bcl2fastq === | ||
A few different versions of bcl2fastq2 are installed across all HPC nodes. The available versions are: bcl2fastq2-v2.15.0.4, | 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-v2.16.0.10, bcl2fastq2-v2.17.1.14. v2.19.0.316 and v2.20.0.422 |
==== Usage ==== | ==== Usage ==== | ||
| Line 9: | Line 9: | ||
[asrini@node61 ~]$ module avail | [asrini@node61 ~]$ module avail | ||
| − | --------------------------------------------------------- /usr/share/Modules/modulefiles --------------------------------------------------------- | + | --------------------------------------------------------------------------------- /usr/share/Modules/modulefiles ---------------------------------------------------------------------------------- |
| − | AllPaths-LG-v49967 | + | AllPaths-LG-v49967 bwa-0.7.10 homer-v4.6 pcre-8.38 R/3.4.3 sratoolkit-2.4.2 |
| − | autoconf-2.69 | + | autoconf-2.69 bzip2-1.0.6 java-sdk-1.6.0 perl5lib R-3.1.1 STAR-2.3.0e |
| − | automake-1.15 | + | 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 | + | 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 | + | bcl2fastq2/v2.15.0.4 circos-0.67-5 kClust-1.0 pkg-config-path R-3.2.2 STAR-hg19 |
| − | bcl2fastq2 | + | bcl2fastq2/v2.16.0.10 cufflinks-2.2.0 ld-library-path plink-1.90b3b R-3.3.0 STAR-mm9 |
| − | bcl2fastq2 | + | 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 ---------------------------------------------------------------- | + | ---------------------------------------------------------------------------------------- /etc/modulefiles ----------------------------------------------------------------------------------------- |
| − | mpich-x86_64 | + | mpich-x86_64 openmpi-x86_64 |
| Line 44: | Line 41: | ||
</pre> | </pre> | ||
| + | |||
| + | '''Note the difference in module usage:''' | ||
| + | |||
| + | <pre> | ||
| + | [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. | ||
| + | |||
| + | |||
| + | </pre> | ||
| + | |||
=== Other Pages === | === Other Pages === | ||
Revision as of 01:38, 16 March 2018
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.
