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changeset 1:75845643f9dd

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Requirement fixes and fixed sample loc file."
author devteam@galaxyproject.org
date Mon, 27 Jan 2014 14:30:21 -0500
parents 70f710e91120
children 664f7d964231
files tool-data/tophat_fusion_blastdb.loc.sample tool_dependencies.xml tophat_fusion_post.xml
diffstat 3 files changed, 12 insertions(+), 32 deletions(-) [+]
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line diff
--- a/tool-data/tophat_fusion_blastdb.loc.sample	Mon Jan 27 13:16:59 2014 -0500
+++ b/tool-data/tophat_fusion_blastdb.loc.sample	Mon Jan 27 14:30:21 2014 -0500
@@ -1,37 +1,13 @@
 #This is a sample file distributed with Galaxy that is used to define a
-#list of nucleotide BLAST databases, using three columns tab separated
+#list of nucleotide BLAST databases for tophat-fusion-post, using fod columns tab separated
 #(longer whitespace are TAB characters):
 #
-#<unique_id>	<database_caption>	<base_name_path>
-#
-#The captions typically contain spaces and might end with the build date.
-#It is important that the actual database name does not have a space in
-#it, and that there are only two tabs on each line.
-#
-#So, for example, if your database is nt and the path to your base name 
-#is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry 
-#would look like this:
-#
-#nt_02_Dec_2009      nt 02 Dec 2009      /depot/data2/galaxy/blastdb/nt/nt.chunk
+#<unique_id>	<dbkey>	<name>	<path>
 #
-#and your /depot/data2/galaxy/blastdb/nt directory would contain all of 
-#your "base names" (e.g.):
-#
-#-rw-r--r--  1 wychung galaxy  23437408 2008-04-09 11:26 nt.chunk.00.nhr
-#-rw-r--r--  1 wychung galaxy   3689920 2008-04-09 11:26 nt.chunk.00.nin
-#-rw-r--r--  1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq
-#...etc...
+# For example:
 #
-#Your blastdb.loc file should include an entry per line for each "base name" 
-#you have stored.  For example:
-#
-#nt_02_Dec_2009		nt 02 Dec 2009		/depot/data2/galaxy/blastdb/nt/nt.chunk
-#wgs_30_Nov_2009	wgs 30 Nov 2009	/depot/data2/galaxy/blastdb/wgs/wgs.chunk
-#test_20_Sep_2008	test 20 Sep 2008	/depot/data2/galaxy/blastdb/test/test
-#...etc...
+# hg19	hg19	hg19-blast	/depot/data2/galaxy/hg19/blastdb/
 #
 #You can download the NCBI provided protein databases like NT from here:
 #ftp://ftp.ncbi.nlm.nih.gov/blast/db/
-#
-#See also blastdb_p.loc which is for any protein BLAST database, and
-#blastdb_d.loc which is for any protein domains databases (like CDD).
\ No newline at end of file
+#
\ No newline at end of file
--- a/tool_dependencies.xml	Mon Jan 27 13:16:59 2014 -0500
+++ b/tool_dependencies.xml	Mon Jan 27 14:30:21 2014 -0500
@@ -3,4 +3,7 @@
     <package name="blast+" version="2.2.28">
         <repository name="package_blast_plus_2_2_28" owner="iuc"/>
     </package>
+    <package name="bowtie2" version="2.1.0">
+        <repository name="package_bowtie2_2_1_0" owner="devteam"/>
+    </package>
 </tool_dependency>
--- a/tophat_fusion_post.xml	Mon Jan 27 13:16:59 2014 -0500
+++ b/tophat_fusion_post.xml	Mon Jan 27 14:30:21 2014 -0500
@@ -2,7 +2,8 @@
     <description>post-processing to identify fusion genes</description>
     <version_command>tophat-fusion-post --version</version_command>
     <requirements>
-        <requirement type="package">tophat2</requirement>
+        <requirement type="package" version="2.2.28">blast+</requirement>
+        <requirement type="package" version="2.1.0">bowtie2</requirement>
     </requirements>
     <command>
         ## Set up tophat_out structure.
@@ -24,8 +25,8 @@
               --non-human
         #end if
 
-	## Bowtie2 indices.
-	${__get_data_table_entry__('bowtie2_indexes', 'dbkey', $accepted_hits.dbkey, 'path')}
+	    ## Bowtie2 indices.
+	    ${__get_data_table_entry__('bowtie2_indexes', 'dbkey', $accepted_hits.dbkey, 'path')}
     </command>
 
     <inputs>