From d2832a877aec713eef45912603e7fc7f1c48beda Mon Sep 17 00:00:00 2001
From: Peter Cock <p.j.a.cock@googlemail.com>
Date: Thu, 16 Feb 2012 12:14:54 +0000
Subject: [PATCH] Enable splitting BLAST jobs up (doesn't work yet)

---
 tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml  | 1 +
 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml  | 1 +
 tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml  | 1 +
 tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml | 1 +
 tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml | 1 +
 5 files changed, 5 insertions(+)

diff --git a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
index 9230ad55531..48ce2156dfc 100644
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
@@ -1,5 +1,6 @@
 <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.11">
     <description>Search nucleotide database with nucleotide query sequence(s)</description>
+    <parallelism method="multi" split_inputs="query" shared_inputs="subject" merge_outputs="output1"></parallelism>
     <version_command>blastn -version</version_command>
     <command interpreter="python">hide_stderr.py
 ## The command is a Cheetah template which allows some Python based syntax.
diff --git a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
index 800171601e9..abcf1182367 100644
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
@@ -1,5 +1,6 @@
 <tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.11">
     <description>Search protein database with protein query sequence(s)</description>
+    <parallelism method="multi" split_inputs="query" shared_inputs="subject" merge_outputs="output1"></parallelism>
     <version_command>blastp -version</version_command>
     <command interpreter="python">hide_stderr.py
 ## The command is a Cheetah template which allows some Python based syntax.
diff --git a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
index 5a54575545b..aa068a3e696 100644
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
@@ -1,5 +1,6 @@
 <tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.11">
     <description>Search protein database with translated nucleotide query sequence(s)</description>
+    <parallelism method="multi" split_inputs="query" shared_inputs="subject" merge_outputs="output1"></parallelism>
     <version_command>blastx -version</version_command>
     <command interpreter="python">hide_stderr.py
 ## The command is a Cheetah template which allows some Python based syntax.
diff --git a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
index b7876c05ff6..f901929fa07 100644
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
@@ -1,5 +1,6 @@
 <tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.11">
     <description>Search translated nucleotide database with protein query sequence(s)</description>
+    <parallelism method="multi" split_inputs="query" shared_inputs="subject" merge_outputs="output1"></parallelism>
     <version_command>tblastn -version</version_command>
     <command interpreter="python">hide_stderr.py
 ## The command is a Cheetah template which allows some Python based syntax.
diff --git a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
index cb1e7f2a1c2..7aef774d050 100644
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
@@ -1,5 +1,6 @@
 <tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.11">
     <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description>
+    <parallelism method="multi" split_inputs="query" shared_inputs="subject" merge_outputs="output1"></parallelism>
     <version_command>tblastx -version</version_command>
     <command interpreter="python">hide_stderr.py
 ## The command is a Cheetah template which allows some Python based syntax.