Changes between Version 1 and Version 2 of cypress/WGSA

Timestamp:

07/14/20 16:44:55 (5 years ago)

Author:

fuji

Comment:

—

cypress/WGSA

@@ -52 +52 @@
 }}}
 
-Now you need a newer version of JavaSDK, to use it, you have to do on a computing node.
+To use a newer version of JavaSDK, you have to login to a computing node.
 
 Start a interactive session:
@@ -64 +64 @@
 Once you get to a computing node, make sure your corrent directory is $WGSA_DIR/snpeff
 
-Download !RefSeq and !Ensembl gene models for !SnpEff:
+Download !RefSeq and Ensembl gene models for !SnpEff:
 
 {{{
+module load java-openjdk/1.8.0
 cd snpEff
 java -jar snpEff.jar download -v hg19
@@ -80 +81 @@
 }}}
 
+Install htslib, which is required for VEP API.
+
+{{{
+mkdir $WGSA_DIR/htslib
+cd $WGSA_DIR/htslib
+wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2
+tar -vxjf htslib-1.9.tar.bz2
+cd htslib-1.9
+make prefix=$WGSA_DIR/htslib install
+}}}
+
+Setup the environmental variables
+
+{{{
+export PATH=$WGSA_DIR/htslib/bin:$PATH
+export CPATH=$WGSA_DIR/htslib/include:$CPATH
+export LD_LIBRARY_PATH=$WGSA_DIR/htslib/lib:$LD_LIBRARY_PATH
+}}}
+
+
 Install VEP (required for annotating indels with VEP or annotating SNVs with VEP on-the-fly)
 
@@ -91 +112 @@
 }}}
 
+Install VEP API to /WGSA/vep and download !RefSeq and Ensembl gene models to $WGSA_DIR/.vep
+{{{
+cd $WGSA_DIR/vep/ensembl-vep-release-94/
+mkdir $WGSA_DIR/.vep
+perl INSTALL.pl -c $WGSA_DIR/.vep --ASSEMBLY GRCh37
+}}}
+Go 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.
+{{{
+perl INSTALL.pl -c $WGSA_DIR/.vep --ASSEMBLY GRCh38
+}}}
+When 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.
+{{{
+chmod 777 $WGSA_DIR/.vep/Plugins
+chmod 777 $WGSA_DIR/.vep/homo_sapiens/94_GRCh37
+chmod 777 $WGSA_DIR/.vep/homo_sapiens/94_GRCh38
+}}}
 
+Install LOFTEE LOF plugin for VEP API
+{{{
+cd $WGSA_DIR/.vep/Plugins
+wget https://github.com/konradjk/loftee/archive/v0.1.1-beta.zip
+unzip -j v0.1.1-beta.zip
+rm v0.1.1-beta.zip
+}}}