Difference between revisions of "HPC:bcl2fastq"
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(Created page with "=== bcl2fastq === bcl2fastq2 v02.14.01.07 is installed across all HPC nodes. ==== Usage ==== bcl2fastq2 can be loaded as a module: <pre> [asrini@node061 ~]$ module load bcl...") |
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=== bcl2fastq === | === bcl2fastq === | ||
| − | bcl2fastq2 | + | 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 ==== | ==== Usage ==== | ||
| − | bcl2fastq2 can be loaded as a module: | + | Any of bcl2fastq2 can be loaded as a module: |
<pre> | <pre> | ||
| − | [asrini@node061 ~]$ module load bcl2fastq2- | + | [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 | [asrini@node061 ~]$ bcl2fastq --version | ||
BCL to FASTQ file converter | BCL to FASTQ file converter | ||
| − | bcl2fastq | + | bcl2fastq v2.17.1.14 |
| − | Copyright (c) 2007- | + | Copyright (c) 2007-2015 Illumina, Inc. |
</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 === | ||
| + | ---- | ||
| + | <div class="mw-collapsible mw-collapsed"> | ||
| + | *[[HPC:FAQ|HPC FAQ ]] | ||
| + | *[[HPC:Login|Connecting to the PMACS cluster]] | ||
| + | *[[HPC:User_Guide|User Guide]] | ||
*[[HPC:Software|Available Software]] | *[[HPC:Software|Available Software]] | ||
| − | *[[HPC: | + | *[[HPC:Archive System|PMACS Archive System]] |
| − | + | </div> | |
| − | |||
Latest revision as of 15:17, 13 August 2019
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.
