# HG changeset patch
# User Daniel Blankenberg <dan@bx.psu.edu>
# Date 1369322498 14400
# Node ID 2c5dc42b31b6159c4382e89bfc38418e88ef354b
# Parent  1a6c1790048eea51e48a7a09eec87a19d735bca9
Populate repository

diff -r 1a6c1790048e -r 2c5dc42b31b6 data_manager/data_manager_sam_fa_index_builder.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_sam_fa_index_builder.py	Thu May 23 11:21:38 2013 -0400
@@ -0,0 +1,71 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+import sys
+import os
+import tempfile
+import optparse
+import subprocess
+
+from galaxy.util.json import from_json_string, to_json_string
+
+CHUNK_SIZE = 2**20
+
+DEFAULT_DATA_TABLE_NAME = "sam_indexes"
+
+def build_sam_index( data_manager_dict, fasta_filename, target_directory, dbkey, data_table_name=DEFAULT_DATA_TABLE_NAME ):
+    #TODO: allow multiple FASTA input files
+    fasta_base_name = os.path.split( fasta_filename )[-1]
+    sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
+    os.symlink( fasta_filename, sym_linked_fasta_filename )
+    
+    args = [ 'samtools', 'faidx' ]
+    args.append( sym_linked_fasta_filename )
+    tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-sam_fa_index_builder-stderr" )
+    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
+    return_code = proc.wait()
+    if return_code:
+        tmp_stderr.flush()
+        tmp_stderr.seek( 0 )
+        sys.stderr.write( "Error building index:\n" )
+        while True:
+            chunk = tmp_stderr.read( CHUNK_SIZE )
+            if not chunk:
+                break
+            sys.stderr.write( chunk )
+        sys.exit( return_code )
+    tmp_stderr.close()
+    data_table_entry = dict( line_type="index", value=dbkey, path=fasta_base_name )
+    _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
+
+def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
+    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+    data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
+    data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
+    return data_manager_dict
+
+def main():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
+    parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
+    parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' )
+    (options, args) = parser.parse_args()
+    
+    filename = args[0]
+    
+    params = from_json_string( open( filename ).read() )
+    target_directory = params[ 'output_data' ][0]['extra_files_path']
+    os.mkdir( target_directory )
+    data_manager_dict = {}
+    
+    if options.fasta_dbkey in [ None, '', '?' ]:
+        raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
+    
+    #build the index
+    build_sam_index( data_manager_dict, options.fasta_filename, target_directory, options.fasta_dbkey,  data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME )
+    
+    #save info to json file
+    open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
+        
+if __name__ == "__main__": main()
diff -r 1a6c1790048e -r 2c5dc42b31b6 data_manager/data_manager_sam_fa_index_builder.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_sam_fa_index_builder.xml	Thu May 23 11:21:38 2013 -0400
@@ -0,0 +1,23 @@
+<tool id="data_manager_sam_fa_index_builder" name="SAM FASTA index" tool_type="manage_data" version="0.0.1">
+    <description>builder</description>
+    <requirements>
+        <requirement type="package" version="0.1.18">samtools</requirement>
+    </requirements>
+    <command interpreter="python">data_manager_sam_fa_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --data_table_name "sam_fa_indexes"</command>
+    <inputs>
+        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
+            <options from_data_table="all_fasta"/>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json"/>
+    </outputs>
+
+    <help>
+
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically. 
+
+    </help>
+</tool>
diff -r 1a6c1790048e -r 2c5dc42b31b6 data_manager_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Thu May 23 11:21:38 2013 -0400
@@ -0,0 +1,20 @@
+<?xml version="1.0"?>
+<data_managers>
+    
+    <data_manager tool_file="data_manager/data_manager_sam_fa_index_builder.xml" id="sam_fa_index_builder" version="0.0.1">
+        <data_table name="sam_fa_indexes">
+            <output>
+                <column name="line_type" />
+                <column name="value" />
+                <column name="path" output_ref="out_file" >
+                    <move type="directory" relativize_symlinks="True">
+                        <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base -->
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}/sam_index/${value}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/sam_index/${value}/${path}</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
+    
+</data_managers>
diff -r 1a6c1790048e -r 2c5dc42b31b6 tool-data/all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Thu May 23 11:21:38 2013 -0400
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>		<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3		/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19		Human (Homo sapiens): hg19 Canonical		/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19		Human (Homo sapiens): hg19 Full			/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
diff -r 1a6c1790048e -r 2c5dc42b31b6 tool-data/sam_fa_indices.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/sam_fa_indices.loc.sample	Thu May 23 11:21:38 2013 -0400
@@ -0,0 +1,28 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a sam_fa_indices.loc file 
+#similar to this one (store it in this directory) that points to 
+#the directories in which those files are stored. The sam_fa_indices.loc 
+#file has this format (white space characters are TAB characters):
+#
+#index	<seq>	<location>
+#
+#So, for example, if you had hg18 indexed stored in 
+#/depot/data2/galaxy/sam/, 
+#then the sam_fa_indices.loc entry would look like this:
+#
+#index	hg18	/depot/data2/galaxy/sam/hg18.fa
+#
+#and your /depot/data2/galaxy/sam/ directory
+#would contain hg18.fa and hg18.fa.fai files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.fa
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.fa.fai
+#
+#Your sam_fa_indices.loc file should include an entry per line for 
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#index	hg18	/depot/data2/galaxy/sam/hg18.fa
+#index	hg19	/depot/data2/galaxy/sam/hg19.fa
diff -r 1a6c1790048e -r 2c5dc42b31b6 tool-data/tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tool_data_table_conf.xml.sample	Thu May 23 11:21:38 2013 -0400
@@ -0,0 +1,12 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+    <!-- Location of SAMTools indexes and other files -->
+    <table name="sam_fa_indexes" comment_char="#">
+        <columns>line_type, value, path</columns>
+        <file path="tool-data/sam_fa_indices.loc" />
+    </table>
+</tables>
diff -r 1a6c1790048e -r 2c5dc42b31b6 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu May 23 11:21:38 2013 -0400
@@ -0,0 +1,6 @@
+<tool_dependency>
+    <package name="samtools" version="0.1.18">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_samtools_0_1_18" owner="devteam" changeset_revision="5f7ec5048224" />
+    </package>
+</tool_dependency>
+