Changes between Version 1 and Version 2 of cypress/WGSA


Ignore:
Timestamp:
Jul 14, 2020 4:44:55 PM (18 months ago)
Author:
fuji
Comment:

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  • cypress/WGSA

    v1 v2  
    5252}}}
    5353
    54 Now you need a newer version of JavaSDK, to use it, you have to do on a computing node.
     54To use a newer version of JavaSDK, you have to login to a computing node.
    5555
    5656Start a interactive session:
     
    6464Once you get to a computing node, make sure your corrent directory is $WGSA_DIR/snpeff
    6565
    66 Download !RefSeq and !Ensembl gene models for !SnpEff:
     66Download !RefSeq and Ensembl gene models for !SnpEff:
    6767
    6868{{{
     69module load java-openjdk/1.8.0
    6970cd snpEff
    7071java -jar snpEff.jar download -v hg19
     
    8081}}}
    8182
     83Install htslib, which is required for VEP API.
     84
     85{{{
     86mkdir $WGSA_DIR/htslib
     87cd $WGSA_DIR/htslib
     88wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2
     89tar -vxjf htslib-1.9.tar.bz2
     90cd htslib-1.9
     91make prefix=$WGSA_DIR/htslib install
     92}}}
     93
     94Setup the environmental variables
     95
     96{{{
     97export PATH=$WGSA_DIR/htslib/bin:$PATH
     98export CPATH=$WGSA_DIR/htslib/include:$CPATH
     99export LD_LIBRARY_PATH=$WGSA_DIR/htslib/lib:$LD_LIBRARY_PATH
     100}}}
     101
     102
    82103Install VEP (required for annotating indels with VEP or annotating SNVs with VEP on-the-fly)
    83104
     
    91112}}}
    92113
     114Install VEP API to /WGSA/vep and download !RefSeq and Ensembl gene models to $WGSA_DIR/.vep
     115{{{
     116cd $WGSA_DIR/vep/ensembl-vep-release-94/
     117mkdir $WGSA_DIR/.vep
     118perl INSTALL.pl -c $WGSA_DIR/.vep --ASSEMBLY GRCh37
     119}}}
     120Go through the steps of the installing process and following the guidance at http://useast.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html. When being asked for the cache files, choose “242 : homo_sapiens_merged_vep_94_GRCh37.tar.gz”. When being asked for fasta files, choose “27 : homo_sapiens”. When being asked for the plugins, choose "7:LOF". The fasta file downloading is required for the current version of WGSA.
     121{{{
     122perl INSTALL.pl -c $WGSA_DIR/.vep --ASSEMBLY GRCh38
     123}}}
     124When being asked for the cache files, choose "243 : homo_sapiens_merged_vep_94_GRCh38.tar.gz". When being asked for fasta files, choose “54: homo_sapiens”. When being asked for the plugins, choose "n" as LOF has already been installed.
     125{{{
     126chmod 777 $WGSA_DIR/.vep/Plugins
     127chmod 777 $WGSA_DIR/.vep/homo_sapiens/94_GRCh37
     128chmod 777 $WGSA_DIR/.vep/homo_sapiens/94_GRCh38
     129}}}
    93130
     131Install LOFTEE LOF plugin for VEP API
     132{{{
     133cd $WGSA_DIR/.vep/Plugins
     134wget https://github.com/konradjk/loftee/archive/v0.1.1-beta.zip
     135unzip -j v0.1.1-beta.zip
     136rm v0.1.1-beta.zip
     137}}}