Mercurial > repos > bgruening > antismash

changeset 26:a5eb6fad2a76 draft

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Uploaded
author bgruening
date Tue, 15 Jul 2014 13:08:21 -0400
parents 99435bb90725
children ab3eff2028f8
files antismash.xml readme.rst readme.txt repository_dependencies.xml src/genecluster_sequence/__init__.py static/images/antismash_html_overview.png static/images/antismash_user_interface.png tool_dependencies.xml
diffstat 8 files changed, 80 insertions(+), 127 deletions(-) [+]
line wrap: on
line diff
--- a/antismash.xml	Fri Oct 18 03:35:17 2013 -0400
+++ b/antismash.xml	Tue Jul 15 13:08:21 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="antismash" name="Secondary Metabolites" version="2.0.2.1">
+<tool id="antismash" name="Secondary Metabolites" version="2.0.2.2">
     <description>and Antibiotics Analysis (antiSMASH)</description>
     <requirements>
         <requirement type="package" version="3.0">hmmer</requirement>
@@ -8,12 +8,18 @@
         <requirement type="package" version="3.8.31">muscle</requirement>
         <requirement type="package">muscle</requirement>
         <requirement type="package" version="1.4.0-post-1">straight.plugin</requirement>
+        <requirement type="package">straight.plugin</requirement>
         <requirement type="package" version="1.62">biopython</requirement>
+        <requirement type="package">biopython</requirement>
         <requirement type="package" version="1.2.6">pyquery</requirement>
+        <requirement type="package">pyquery</requirement>
         <requirement type="package" version="0.1.2">helperlibs</requirement>
+        <requirement type="package">helperlibs</requirement>
         <requirement type="package" version="0.9">cssselect</requirement>
+        <requirement type="package">cssselect</requirement>
         <requirement type="package" version="2.0.2">antismash</requirement>
         <requirement type="package">antismash</requirement>
+        <requirement type="package">glimmer</requirement>
     </requirements>
     <command>
         #import os, glob
@@ -28,7 +34,7 @@
         ln -s $infile #echo 'input_tempfile.' + $file_extension#;
         mkdir -p $outputfolder;
         run_antismash.py 
-            --cpus 12
+            --cpus "\${GALAXY_SLOTS:-12}"
             --enable $types
             --input-type 'nucl'
             $smcogs
@@ -44,7 +50,7 @@
                 --pfamdir $pfam_database.fields.path
             #end if
 
-            --debug
+            ##--debug
 
             --disable-embl
             --outputfolder $outputfolder
@@ -128,7 +134,7 @@
             help="(--full-hmmer)"
             truevalue="--full-hmmer" falsevalue="" checked="false" />
 
-        <param name="inclusive" type="boolean" label="Use inclusive algorithm for cluster detection"
+        <param name="inclusive" type="boolean" label="Use Cimermancic et al. algorithm for cluster detection"
             help="(--inclusive)"
             truevalue="--inclusive" falsevalue="" checked="false" />
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Tue Jul 15 13:08:21 2014 -0400
@@ -0,0 +1,65 @@
+Galaxy wrapper for AntiSmash
+=====================================
+
+This wrapper is copyright 2012-2014 by Björn Grüning.
+
+This is a wrapper for the command line tool of antiSMASH.
+
+antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.
+It integrates and cross-links with a large number of in silico secondary metabolite analysis tools.
+
+http://antismash.secondarymetabolites.org/
+
+Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, Rainer Breitling & Eriko Takano (2011).
+antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. Nucleic Acids Research 39: W339-W346.
+
+
+Installation
+============
+
+Galaxy should be able to automatically install the dependencies, i.e. the
+'package_hmmer_3_0' or 'package_blast_plus_2_2_28' repository.
+
+You must tell Galaxy about any system level Pfam databases using the configuration
+file antismash.loc.
+
+You can download the Pfam provided databases as compressed archives from here:
+
+* ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/
+
+
+External Data
+=============
+
+The antismash.loc file contains the path to a Pfam database.
+For any other tool that also uses a Pfam database *.log file, you can sync or link both *.loc files.
+
+
+
+History
+=======
+
+v0.1 - Initial public release
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
--- a/readme.txt	Fri Oct 18 03:35:17 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,81 +0,0 @@
-Galaxy wrapper for AntiSmash
-=====================================
-
-This wrapper is copyright 2012 by Björn Grüning.
-
-This is a wrapper for the command line tool of antiSMASH.
-
-antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.
-It integrates and cross-links with a large number of in silico secondary metabolite analysis tools.
-
-http://antismash.secondarymetabolites.org/
-
-Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, Rainer Breitling & Eriko Takano (2011).
-antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. Nucleic Acids Research 39: W339-W346.
-
-
-Installation
-============
-
-Currently these wrapper is tested with version 1.1 and the modified version of antismash.py included in that repository.
-
-Install or downlaod antiSMASH from:
-
-
-https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.x86_64.tar.bz2
-
-
-... and follow the instructions.
-Please replace the antismash.py file with the one inlcuded in that repository.
-Edit the following lines in multi_antiSMASH_wrapper.py and antiSMASH_wrapper.py and adopt it to your installation.
-
-blastdbpath = '/home/galaxy/bin/antismash-1.1.0/db'
-pfamdbpath = '/home/galaxy/bin/antismash-1.1.0/db'
-antismash_path = '/home/galaxy/bin/antismash-1.1.0/antismash.py'
-
-
-To install the wrapper copy the antiSMASH folder in the galaxy tools
-folder and modify the tools_conf.xml file to make the tool available to Galaxy.
-For example:
-
-<section name="PKS-NRPS prediction" id="pks-nrps_prediction">
-    <tool file="pks-nrps/tools/antiSMASH/antiSMASH.xml" />
-    <tool file="pks-nrps/tools/antiSMASH/multi_antiSMASH.xml" />
-</section>
-
-
-external Data
-=============
-
-The antismash.loc file contains the path to a PFAM database.
-For any other tool that also uses a PFAM database *.log file, you can sync or link both *.loc files.
-
-
-
-History
-=======
-
-v0.1 - Initial public release
-
-
-Wrapper Licence (MIT/BSD style)
-===============================
-
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
-
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
-
--- a/repository_dependencies.xml	Fri Oct 18 03:35:17 2013 -0400
+++ b/repository_dependencies.xml	Tue Jul 15 13:08:21 2014 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="AntiSmash requires the Galaxy applicable data formats used by Emboss tools, especially genbank.">
-    <repository changeset_revision="9f36ad2af086" name="emboss_datatypes" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="9f36ad2af086" name="emboss_datatypes" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>
--- a/src/genecluster_sequence/__init__.py	Fri Oct 18 03:35:17 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-#!/usr/bin/env python
-
-"""
-    antiSMASH 2.0 output plugin to write all cluster proteins to a file (*_genecluster_proteins.fa)
-"""
-import logging
-import textwrap
-from os import path
-from antismash import utils
-
-name = "genecluster_proteins"
-short_description = "Ouptut gene clusters as FASTA sequences"
-# Output plugins are sorted by priority, lower numbers get run first
-priority = 9
-
-def write(seq_records, options):
-    """Write all cluster proteins to a file
-
-    Args:
-        seq_records (iterable): An iterable containing Bio.SeqRecords
-        options (argparse.Namespace): The options passed to the program
-    """
-    basename = seq_records[0].id
-    output_name = path.join(options.outputfoldername, "%s_genecluster_proteins.fa" % basename)
-    logging.debug("Writing seq_records to %r" % output_name)
-
-    with open(output_name, 'w+') as handle:
-        for seq_record in seq_records:
-            clusters = utils.get_cluster_features(seq_record)
-            for cluster in clusters:
-                clustertype = utils.get_cluster_type(cluster)
-                clusternr = utils.get_cluster_number(cluster)
-                for feature in utils.get_cluster_cds_features(cluster, seq_record):
-                    qual = feature.qualifiers
-                    fasta_header = '>%s:%s %s #%s - %s\n' % (qual['locus_tag'][0], qual['protein_id'][0], clustertype, clusternr, qual['product'][0])
-                    handle.write( fasta_header )
-                    handle.write( '%s\n' % '\n'.join( textwrap.wrap(qual['translation'][0], 60) ) )
Binary file static/images/antismash_html_overview.png has changed
Binary file static/images/antismash_user_interface.png has changed
--- a/tool_dependencies.xml	Fri Oct 18 03:35:17 2013 -0400
+++ b/tool_dependencies.xml	Tue Jul 15 13:08:21 2014 -0400
@@ -1,16 +1,16 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="blast+" version="2.2.28">
-        <repository changeset_revision="5a449da71d08" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="6f6a8be93479" name="package_blast_plus_2_2_28" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="hmmer" version="3.0">
-        <repository changeset_revision="a44693e3a2c4" name="package_hmmer_3_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a44693e3a2c4" name="package_hmmer_3_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="muscle" version="3.8.31">
-        <repository changeset_revision="83bd107a5300" name="package_muscle_3_8_31" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a8912a41ecc8" name="package_muscle_3_8_31" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="biopython" version="1.62">
-        <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 
     <package name="helperlibs" version="0.1.2">