changeset 0:26e3ae5f74ed draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
author devteam
date Fri, 02 Oct 2015 17:32:37 -0400
parents
children 298d15849a14
files README data_manager/twobit_builder.py data_manager/twobit_builder.xml data_manager_conf.xml tool-data/alignseq.loc.sample tool-data/all_fasta.loc.sample tool-data/lastz_seqs.loc.sample tool-data/twobit.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml
diffstat 10 files changed, 326 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Fri Oct 02 17:32:37 2015 -0400
@@ -0,0 +1,1 @@
+TODO
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/twobit_builder.py	Fri Oct 02 17:32:37 2015 -0400
@@ -0,0 +1,92 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+import sys, os, tempfile, optparse, uuid, subprocess
+
+from json import loads, dumps
+
+
+CHUNK_SIZE = 2**20 #1mb
+
+def get_id_name( params, dbkey, fasta_description=None):
+    #TODO: ensure sequence_id is unique and does not already appear in location file
+    sequence_id = params['param_dict']['sequence_id']
+    if not sequence_id:
+        sequence_id = dbkey #uuid.uuid4() generate and use an uuid
+    
+    sequence_name = params['param_dict']['sequence_name']
+    if not sequence_name:
+        sequence_name = fasta_description
+        if not sequence_name:
+            sequence_name = dbkey
+    return sequence_id, sequence_name
+
+def build_twobit( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name ):
+    twobit_base_name = "%s.2bit" % ( sequence_id )
+    twobit_filename = os.path.join( target_directory, twobit_base_name )
+    
+    args = [ 'faToTwoBit', fasta_filename, twobit_filename ]
+    tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-twobit-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)
+        print >> sys.stderr, "Error building index:"
+        while True:
+            chunk = tmp_stderr.read( CHUNK_SIZE )
+            if not chunk:
+                break
+            sys.stderr.write( chunk )
+        sys.exit( return_code )
+    tmp_stderr.close()
+    #lastz_seqs
+    data_table_entry = dict( value=sequence_id, name=sequence_name, path=twobit_base_name )
+
+    _add_data_table_entry( data_manager_dict, "lastz_seqs", data_table_entry )
+    #twobit.loc
+    data_table_entry = dict( value=sequence_id, path=twobit_base_name )
+
+    _add_data_table_entry( data_manager_dict, "twobit", data_table_entry )
+    #alignseq
+    data_table_entry = dict( type="seq", value=sequence_id, path=twobit_base_name )
+
+    _add_data_table_entry( data_manager_dict, "alignseq_seq", 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( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
+    (options, args) = parser.parse_args()
+    
+    filename = args[0]
+    
+    params = loads( open( filename ).read() )
+
+    target_directory = params[ 'output_data' ][0]['extra_files_path']
+    os.mkdir( target_directory )
+    data_manager_dict = {}
+    
+    dbkey = options.fasta_dbkey
+    
+    if dbkey in [ None, '', '?' ]:
+        raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
+    
+    sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description )
+    
+    #build the index
+    build_twobit( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name )
+    
+    #save info to json file
+    open( filename, 'wb' ).write( dumps( data_manager_dict ) )
+        
+if __name__ == "__main__": main()
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/twobit_builder.xml	Fri Oct 02 17:32:37 2015 -0400
@@ -0,0 +1,35 @@
+<tool id="twobit_builder_data_manager" name="TwoBit" tool_type="manage_data" version="0.0.1">
+    <requirements>
+        <requirement type="package" version="312">ucsc_tools</requirement>
+    </requirements>
+    <description>builder</description>
+    <command interpreter="python">twobit_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}"</command>
+    <inputs>
+        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
+            <options from_data_table="all_fasta"/>
+        </param>
+        <param type="text" name="sequence_name" value="" label="Name of sequence" />
+        <param type="text" name="sequence_id" value="" label="ID for sequence" />
+        
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="all_fasta_source" value="sacCer2"/>
+            <param name="sequence_name" value=""/>
+            <output name="sequence_id" file="data_manager_two_bit_out_1.dat"/>
+        </test>
+    </tests>
+
+    <help>
+
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically. 
+
+    </help>
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Fri Oct 02 17:32:37 2015 -0400
@@ -0,0 +1,40 @@
+<?xml version="1.0"?>
+<data_managers>
+    
+    <data_manager tool_file="data_manager/twobit_builder.xml" id="twobit_builder" version="0.0.1">
+        <data_table name="lastz_seqs">
+            <output>
+                <column name="value" />
+                <column name="name" />
+                <column name="path" output_ref="out_file" >
+                    <move type="file">
+                        <source>${path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}/seq/${path}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/seq/${path}</value_translation>
+                </column>
+            </output>
+        </data_table>
+        
+        <data_table name="twobit">
+            <output>
+                <column name="value" />
+                <column name="path" output_ref="out_file" ><!-- move happens above -->
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/seq/${path}</value_translation>
+                </column>
+            </output>
+        </data_table>
+        
+        <data_table name="alignseq_seq">
+            <output>
+                <column name="type" /><!-- always seq -->
+                <column name="value" /><!-- also dbkey -->
+                <column name="path" output_ref="out_file" ><!-- move happens above -->
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/seq/${path}</value_translation>
+                </column>
+            </output>
+        </data_table>
+        
+    </data_manager>
+    
+</data_managers>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/alignseq.loc.sample	Fri Oct 02 17:32:37 2015 -0400
@@ -0,0 +1,57 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use alignment data stored as axt files (lines starting with "align")
+#or nib files (lines starting with "seq").  You will need to index 
+#them and then create an alignseq.loc file similar to this one (store
+#it in this directory) that points to the directories in which those 
+#alignments are stored.  The "align" data referred to by the alignseq.loc 
+#file has this format (white space characters are TAB characters):
+#
+#align	<build1>	<build2>	<dir>
+#
+#So, for example, if you had hg18/bosTau2 alignment files stored in 
+#/depot/data2/galaxy/hg18/align/bosTau2, then the alignseq.loc entry 
+#would look like this:
+#
+#align	hg18	bosTau2	/depot/data2/galaxy/hg18/align/bosTau2
+#
+#and your /depot/data2/galaxy/hg18/align/bosTau2 directory would 
+#contain all of your alignment files (e.g.):
+#
+#-rw-rw-r--   1 nate   galaxy 151842783 2006-01-08 01:00 chr10.axt
+#-rw-rw-r--   1 nate   galaxy     79575 2006-01-08 01:00 chr10_random.axt
+#-rw-rw-r--   1 nate   galaxy 155015634 2006-01-08 01:01 chr11.axt
+#...etc...
+#
+#Your alignseq.loc file should include an entry per line for each alignment 
+#file you have stored.  For example:
+#
+#align anoGam1 dm1 /depot/data2/galaxy/anoGam1/align/dm1
+#align anoGam1 dm2 /depot/data2/galaxy/anoGam1/align/dm2
+#align canFam1 hg17 /depot/data2/galaxy/canFam1/align/hg17
+#...etc...
+#
+#The "seq" data referred to by the alignseq.loc file has this 
+#format (white space characters are TAB characters):
+#
+#seq	<build1>	<dir>
+#
+#So, for example, if you had anoGam1 sequence files stored in
+#/depot/data2/galaxy/anoGam1/seq, then the alignseq.loc entry
+#would look like this:
+#
+#seq anoGam1 /depot/data2/galaxy/anoGam1/seq
+#and your seq anoGam1 /depot/data2/galaxy/anoGam1/seq directory would
+#contain all of your sequence files (e.g.):
+#
+#-rw-rw-r-- 1 nate galaxy 24397551 2006-06-26 12:51 chr2L.nib
+#-rw-rw-r-- 1 nate galaxy 31362964 2006-06-26 12:51 chr2R.nib
+#-rw-rw-r-- 1 nate galaxy 20642013 2006-06-26 12:51 chr3L.nib
+#-rw-rw-r-- 1 nate galaxy 26636071 2006-06-26 12:51 chr3R.nib
+#
+#Your alignseq.loc file should include an entry per line for each sequence
+#file you have stored.  For example:
+#
+#seq anoGam1 /depot/data2/galaxy/anoGam1/seq
+#seq bosTau2 /depot/data2/galaxy/bosTau2/seq
+#seq bosTau3 /depot/data2/galaxy/bosTau3/seq
+#...etc...
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Fri Oct 02 17:32:37 2015 -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.
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/lastz_seqs.loc.sample	Fri Oct 02 17:32:37 2015 -0400
@@ -0,0 +1,30 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of 2bit genome files for use with Lastz. You will
+#need to supply these files and then create a lastz_seqs.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The lastz_seqs.loc
+#file has this format (white space characters are TAB characters):
+#
+#<unique_build_id>	<display_name>		<file_path>
+#
+#So, for example, if your lastz_seqs.loc began like this:
+#
+#hg18	Human (Homo sapiens): hg18		/depot/data2/galaxy/twobit/hg18.2bit
+#hg19	Human (Homo sapiens): hg19		/depot/data2/galaxy/twobit/hg19.2bit
+#mm9	Mouse (Mus musculus): mm9		/depot/data2/galaxy/twobit/mm9.2bit
+#
+#then your /depot/data2/galaxy/twobit/ directory
+#would need to contain the following 2bit files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.2bit
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg19.2bit
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 mm9.2bit
+#
+#Your lastz_seqs.loc file should include an entry per line for 
+#each file you have stored that you want to be available. Note that 
+#your files should all have the extension '2bit'.
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. 
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/twobit.loc.sample	Fri Oct 02 17:32:37 2015 -0400
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that is used by some
+#tools.  The twobit.loc file has this format (white space characters 
+#are TAB characters):
+#
+#<Build>	<FullPathToFile>
+#
+#So, for example, if you had droPer1 twobit files stored in 
+#/depot/data2/galaxy/droPer1/, then the twobit.loc entry 
+#would look like this:
+#
+#droPer1	/depot/data2/galaxy/droPer1/droPer1.2bit
+#
+#and your /depot/data2/galaxy/droPer1/ directory would 
+#contain all of your twobit files (e.g.):
+#
+#-rw-rw-r--   1 nate   galaxy 48972650 2007-05-04 11:27 droPer1.2bit
+#...etc...
+#
+#Your twobit.loc file should include an entry per line for each twobit 
+#file you have stored.  For example:
+#
+#droPer1	/depot/data2/galaxy/droPer1/droPer1.2bit
+#apiMel2	/depot/data2/galaxy/apiMel2/apiMel2.2bit
+#droAna1	/depot/data2/galaxy/droAna1/droAna1.2bit
+#droAna2	/depot/data2/galaxy/droAna2/droAna2.2bit
+#...etc...
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Oct 02 17:32:37 2015 -0400
@@ -0,0 +1,21 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<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>
+    <!-- Locations of 2bit sequence files for use in Lastz -->
+    <table name="lastz_seqs" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/lastz_seqs.loc" />
+    </table>
+    <table name="twobit" comment_char="#">
+        <columns>value, path</columns>
+        <file path="tool-data/twobit.loc" />
+    </table>
+    <table name="alignseq_seq" comment_char="#">
+        <columns>type, value, path</columns>
+        <file path="tool-data/alignseq.loc" />
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Oct 02 17:32:37 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="ucsc_tools" version="312">
+      <repository changeset_revision="ceda74761368" name="package_ucsc_tools_312" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>