Mercurial > repos > davidvanzessen > igblastn_immunerepertoire_igg

changeset 1:7b0d9c107680 draft

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Uploaded
author davidvanzessen
date Thu, 23 Jan 2014 08:29:40 -0500
parents d52f6a986108
children 364b169ffb30
files combined.sh database.zip tool_dependencies.xml
diffstat 3 files changed, 11 insertions(+), 26 deletions(-) [+]
line wrap: on
line diff
--- 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 "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html
 echo "<tr><td>-----------------------------------</td></tr>" >> $html
 
+
+
 function blastAndParse {
 	echo "<tr><td>Starting blast of sample $3 of patient $2</td></tr>" >> $html
 	echo "$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 "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html
 
 	echo "<tr><td>Starting parse of sample $3 of patient $2</td></tr>" >> $html
Binary file database.zip has changed
--- a/tool_dependencies.xml	Thu Jan 23 08:22:28 2014 -0500
+++ b/tool_dependencies.xml	Thu Jan 23 08:29:40 2014 -0500
@@ -6,35 +6,15 @@
 	<package name="igBlastn" version="1.0.0"> 
         <install version="1.0">
             <actions>
-            	<action type="download_by_url" target_filename="ncbi-igblast-1.0.0-x64-linux.tar.gz">
-            		ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.0.0/ncbi-igblast-1.0.0-x64-linux.tar.gz
-            	</action>
-            	
-            	
-            	<action type="move_directory_files">
-		    		<source_directory>ncbi-igblast-1.0.0</source_directory>
-			   		<destination_directory>$INSTALL_DIR/ncbi-igblast-1.0.0</destination_directory>
-	       		</action>
-                <action type="set_environment">
-                	<environment_variable name="IGDATA" action="set_to">$INSTALL_DIR/ncbi-igblast-1.0.0</environment_variable>
-                </action>
+            	<action type="shell_command">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</action>
+            	<action type="shell_command">tar zxvf $INSTALL_DIR/ncbi-igblast-1.0.0-x64-linux.tar.gz -C $INSTALL_DIR</action>
                 <action type="set_environment">
                 	<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/ncbi-igblast-1.0.0/bin</environment_variable>
                 </action>
-
-                <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data</action>
-                <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</action>
-                                
-                <action type="shell_command">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"</action>
-                
-                <action type="shell_command">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"</action>
-                
-                <action type="shell_command">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"</action>
-            	
             </actions>
         </install>
         <readme>
-		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.
         </readme>
     </package>
-</tool_dependency>
+</tool_dependency>
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