# HG changeset patch # User davidvanzessen # Date 1390483780 18000 # Node ID 7b0d9c107680a441e46119127c7cf10853873bb7 # Parent d52f6a9861080c1dc4eae14eca0ff9516410adbe Uploaded diff -r d52f6a986108 -r 7b0d9c107680 combined.sh --- a/combined.sh Thu Jan 23 08:22:28 2014 -0500 +++ b/combined.sh Thu Jan 23 08:29:40 2014 -0500 @@ -1,6 +1,9 @@ #!/bin/bash -#export IGDATA=/home/david/tmp/ncbi-igblast-1.0.0; +mkdir $PWD/igblastdatabase +unzip $dir/database.zip -d $PWD/igblastdatabase/ + +export IGDATA=$PWD/igblastdatabase/ clonalType=${@:(-3):1} html=${@:(-2):1} @@ -12,10 +15,12 @@ echo "

Progress

" > $html echo "" >> $html + + function blastAndParse { echo "" >> $html echo "$IGDATA/bin/igblastn -germline_db_V $IGDATA/database/human_gl_V -germline_db_J $IGDATA/database/human_gl_J -germline_db_D $IGDATA/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $IGDATA/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4" - $IGDATA/bin/igblastn -germline_db_V $IGDATA/database/human_gl_V -germline_db_J $IGDATA/database/human_gl_J -germline_db_D $IGDATA/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $IGDATA/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4 + $IGDATA/bin/igblastn -germline_db_V $PWD/igblastdatabase/database/human_gl_V -germline_db_J $PWD/igblastdatabase/database/human_gl_J -germline_db_D $PWD/igblastdatabase/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $PWD/igblastdatabase/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4 echo "" >> $html echo "" >> $html diff -r d52f6a986108 -r 7b0d9c107680 database.zip Binary file database.zip has changed diff -r d52f6a986108 -r 7b0d9c107680 tool_dependencies.xml --- a/tool_dependencies.xml Thu Jan 23 08:22:28 2014 -0500 +++ b/tool_dependencies.xml Thu Jan 23 08:29:40 2014 -0500 @@ -6,35 +6,15 @@ - - ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.0.0/ncbi-igblast-1.0.0-x64-linux.tar.gz - - - - - ncbi-igblast-1.0.0 - $INSTALL_DIR/ncbi-igblast-1.0.0 - - - $INSTALL_DIR/ncbi-igblast-1.0.0 - + wget ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.0.0/ncbi-igblast-1.0.0-x64-linux.tar.gz -P $INSTALL_DIR + tar zxvf $INSTALL_DIR/ncbi-igblast-1.0.0-x64-linux.tar.gz -C $INSTALL_DIR $INSTALL_DIR/ncbi-igblast-1.0.0/bin - - $INSTALL_DIR/ncbi-igblast-1.0.0/internal_data - $INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human - - wget -r -np -nH --cut-dirs=4 -R index.html -P $INSTALL_DIR/ncbi-igblast-1.0.0 "ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data" - - wget -r -np -nH --cut-dirs=4 -R index.html -P $INSTALL_DIR/ncbi-igblast-1.0.0 "ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/database" - - wget -r -np -nH --cut-dirs=4 -R index.html -P $INSTALL_DIR/ncbi-igblast-1.0.0 "ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/optional_file" - - Downloads igBlast with the latest database provided by NCBI, output may change depending on the database available at ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/ + Downloads the igblastn-1.0.0 executable from NCBI and uses a fixed database included in this tool. - + \ No newline at end of file
info
-----------------------------------
Starting blast of sample $3 of patient $2
Finished blast of sample $3 of patient $2
Starting parse of sample $3 of patient $2