| Previous changeset 4:c8c04cd07ca0 (2013-02-20) Next changeset 6:872cf247c899 (2013-09-23) |
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Commit message:
Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions! |
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modified:
tool-data/blast2go.loc.sample |
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added:
tools/blast2go/blast2go.py tools/blast2go/blast2go.txt tools/blast2go/blast2go.xml tools/blast2go/repository_dependencies.xml |
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removed:
tools/ncbi_blast_plus/blast2go.py tools/ncbi_blast_plus/blast2go.txt tools/ncbi_blast_plus/blast2go.xml tools/ncbi_blast_plus/repository_dependencies.xml |
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| diff -r c8c04cd07ca0 -r e4419efbefad tool-data/blast2go.loc.sample --- a/tool-data/blast2go.loc.sample Wed Feb 20 13:33:47 2013 -0500 +++ b/tool-data/blast2go.loc.sample Fri Feb 22 08:47:27 2013 -0500 |
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| @@ -11,6 +11,14 @@ # public database they host in Spain. We also strongly recommend # configuring a local Blast2GO database. # -Local_2011_May Local database (May 2011) /opt/b2g4pipe/Local_2011_May.properties -Spain_2010_May Database in Spain (May 2010) /opt/b2g4pipe/Spain_2010_May.properties -Spain_2011_June Database in Spain (June 2011) /opt/b2g4pipe/Spain_2011_June.properties +# The property filenames can be fullied qualified paths like +# /opt/b2g4pipe/Spain_2012_August.properties or provided they are +# in the same folder as the Blast2GO JAR file, just the filename +# like Spain_2012_August.properties instead. This is intended to +# make migrating between versions of Blast2GO easier (as the +# property files change between versions), and simpler overall. +# +Local_2011_May Local database (May 2011) Local_2011_May.properties +Spain_2010_May Database in Spain (May 2010) Spain_2010_May.properties +Spain_2011_June Database in Spain (June 2011) Spain_2011_June.properties +Spain_2012_August Database in Spain (August 2012) Spain_2012_August.properties |
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| diff -r c8c04cd07ca0 -r e4419efbefad tools/blast2go/blast2go.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/blast2go/blast2go.py Fri Feb 22 08:47:27 2013 -0500 |
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| @@ -0,0 +1,173 @@ +#!/usr/bin/env python +"""Galaxy wrapper for Blast2GO for pipelines, b2g4pipe v2.5. + +This script takes exactly three command line arguments: + * Input BLAST XML filename + * Blast2GO properties filename (settings file) + * Output tabular filename + +The properties filename can be a fully qualified path, but if not +this will look next to the blast2go.jar file. + +Sadly b2g4pipe (at least v2.3.5 to v2.5.0) cannot cope with current +style large BLAST XML files (e.g. from BLAST 2.2.25+), so we reformat +these to avoid it crashing with a Java heap space OutOfMemoryError. + +As part of this reformatting, we check for BLASTP or BLASTX output +(otherwise raise an error), and print the query count. + +It then calls the Java command line tool, and moves the output file to +the location Galaxy is expecting, and removes the tempory XML file. +""" +import sys +import os +import subprocess + +#You may need to edit this to match your local setup, +#blast2go_jar = "/opt/b2g4pipe/blast2go.jar" +blast2go_jar = "/opt/b2g4pipe_v2.5/blast2go.jar" + + +def stop_err(msg, error_level=1): + """Print error message to stdout and quit with given error level.""" + sys.stderr.write("%s\n" % msg) + sys.exit(error_level) + +if len(sys.argv) != 4: + stop_err("Require three arguments: XML filename, properties filename, output tabular filename") + +xml_file, prop_file, tabular_file = sys.argv[1:] + +#We should have write access here: +tmp_xml_file = tabular_file + ".tmp.xml" + +if not os.path.isfile(blast2go_jar): + stop_err("Blast2GO JAR file not found: %s" % blast2go_jar) + +if not os.path.isfile(xml_file): + stop_err("Input BLAST XML file not found: %s" % xml_file) + +if not os.path.isfile(prop_file): + tmp = os.path.join(os.path.split(blast2go_jar)[0], prop_file) + if os.path.isfile(tmp): + #The properties file seems to have been given relative to the JAR + prop_file = tmp + else: + stop_err("Blast2GO configuration file not found: %s" % prop_file) + del tmp + +def prepare_xml(original_xml, mangled_xml): + """Reformat BLAST XML to suit Blast2GO. + + Blast2GO can't cope with 1000s of <Iteration> tags within a + single <BlastResult> tag, so instead split this into one + full XML record per interation (i.e. per query). This gives + a concatenated XML file mimicing old versions of BLAST. + + This also checks for BLASTP or BLASTX output, and outputs + the number of queries. Galaxy will show this as "info". + """ + in_handle = open(original_xml) + footer = " </BlastOutput_iterations>\n</BlastOutput>\n" + header = "" + while True: + line = in_handle.readline() + if not line: + #No hits? + stop_err("Problem with XML file?") + if line.strip() == "<Iteration>": + break + header += line + + if "<BlastOutput_program>blastx</BlastOutput_program>" in header: + print "BLASTX output identified" + elif "<BlastOutput_program>blastp</BlastOutput_program>" in header: + print "BLASTP output identified" + else: + in_handle.close() + stop_err("Expect BLASTP or BLASTX output") + + out_handle = open(mangled_xml, "w") + out_handle.write(header) + out_handle.write(line) + count = 1 + while True: + line = in_handle.readline() + if not line: + break + elif line.strip() == "<Iteration>": + #Insert footer/header + out_handle.write(footer) + out_handle.write(header) + count += 1 + out_handle.write(line) + + out_handle.close() + in_handle.close() + print "Input has %i queries" % count + + +def run(cmd): + #Avoid using shell=True when we call subprocess to ensure if the Python + #script is killed, so too is the child process. + try: + child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + except Exception, err: + stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) + #Use .communicate as can get deadlocks with .wait(), + stdout, stderr = child.communicate() + return_code = child.returncode + + #keep stdout minimal as shown prominently in Galaxy + #Record it in case a silent error needs diagnosis + if stdout: + sys.stderr.write("Standard out:\n%s\n\n" % stdout) + if stderr: + sys.stderr.write("Standard error:\n%s\n\n" % stderr) + + error_msg = None + if return_code: + cmd_str = " ".join(cmd) + error_msg = "Return code %i from command:\n%s" % (return_code, cmd_str) + elif "Database or network connection (timeout) error" in stdout+stderr: + error_msg = "Database or network connection (timeout) error" + elif "Annotation of 0 seqs with 0 annots finished." in stdout+stderr: + error_msg = "No sequences processed!" + + if error_msg: + print error_msg + stop_err(error_msg) + + +blast2go_classpath = os.path.split(blast2go_jar)[0] +assert os.path.isdir(blast2go_classpath) +blast2go_classpath = "%s/*:%s/ext/*:" % (blast2go_classpath, blast2go_classpath) + +prepare_xml(xml_file, tmp_xml_file) +#print "XML file prepared for Blast2GO" + +#We will have write access wherever the output should be, +#so we'll ask Blast2GO to use that as the stem for its output +#(it will append .annot to the filename) +cmd = ["java", "-cp", blast2go_classpath, "es.blast2go.prog.B2GAnnotPipe", + "-in", tmp_xml_file, + "-prop", prop_file, + "-out", tabular_file, #Used as base name for output files + "-annot", # Generate *.annot tabular file + #NOTE: For v2.3.5 must use -a, for v2.5 must use -annot instead + #"-img", # Generate images, feature not in v2.3.5 + ] +#print " ".join(cmd) +run(cmd) + +#Remove the temp XML file +os.remove(tmp_xml_file) + +out_file = tabular_file + ".annot" +if not os.path.isfile(out_file): + stop_err("ERROR - No output annotation file from Blast2GO") + +#Move the output file where Galaxy expects it to be: +os.rename(out_file, tabular_file) + +print "Done" |
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| diff -r c8c04cd07ca0 -r e4419efbefad tools/blast2go/blast2go.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/blast2go/blast2go.txt Fri Feb 22 08:47:27 2013 -0500 |
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| @@ -0,0 +1,153 @@ +Galaxy wrapper for Blast2GO for pipelines, b2g4pipe +=================================================== + +This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute +(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. +See the licence text below. + +This is a wrapper for the command line Java tool b2g4pipe v2.5, +Blast2GO for pipelines. See: + +S. Götz et al. +High-throughput functional annotation and data mining with the Blast2GO suite. +Nucleic Acids Res. 36(10):3420–3435, 2008. +http://dx.doi.org/10.1093/nar/gkn176 + +A. Conesa and S. Götz. +Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics. +Int. J. Plant Genomics. 619832, 2008. +http://dx.doi.org/10.1155/2008/619832 + +A. Conesa et al. +Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. +Bioinformatics 21:3674-3676, 2005. +http://dx.doi.org/10.1093/bioinformatics/bti610 + +http://www.blast2go.org/ + + + +Installation +============ + +The main dependency is b2g4pipe which must be installed manually. Also we +strongly recommend installing a local Blast2GO database as well (see the +intructions below about the blast2go.loc file). At the time of writing, +the current version is b2g4pipe v2.5 which is available here: + +http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip + +You can change the path by editing the definition near the start of the Python +script blast2go.py, but by default it expects the underlying tool to be here: + +/opt/b2g4pipe_v2.5/blast2go.jar + +Installation of the Galaxy wrapper should work automatically via the Galaxy +Tool Shed, including the dependency on 'blast_datatypes' for the 'blastxml' +file format definition. To install the wrapper manually, first install +'blast_datatypes', then copy or move the following files under the Galaxy +tools folder, e.g. in a tools/blast2go/ folder: + +* blast2go.xml (the Galaxy tool definition) +* blast2go.py (the Python wrapper script) +* blast2go.txt (this README file) + +For a manual installation of the wrapper you will also need to modify the +tools_conf.xml file to tell Galaxy to offer the tool. We suggest putting +it next to the NCBI BLAST+ wrappers. Just add the line: + +<tool file="blast2go/blast2go.xml" /> + +As part of setting up b2g4pipe you will need to setup one or more Blast2GO +property files which tell the tool which database to use etc. The example +b2gPipe.properties provided with b2g4pipe is often out of date. The current +server IP address and database name may given on the Blast2GO website, or +can be found by running the latest GUI version via Java web-start, and +looking under the tools/options menu. These property files can be anywhere +accessable to the Galaxy Unix user, we put them with the JAR file etc. + +You must tell Galaxy about these Blast2GO property files so that they can be +offered to the user. Copy file blast2go.loc.sample to tool-data/blast2go.loc +under the Galaxy folder and edit this to match your installation. This must +be plain text, tab separated, with three columns: + +(1) ID for the setup, e.g. Spain_2012_August +(2) Description for the setup, e.g. Database in Spain (August 2012) +(3) Properties filename for the setup, e.g. /opt/b2g4pipe/Spain_2012_August.properties + +Avoid including "Blast2GO" in the description (column 2) as this text will be +included in the automatically assigned output dataset name. The blast2go.loc +file allows you to customise the database setup. If for example you have a local +Blast2GO server running (which we recommend for speed), and you want this to be +the default setting, include it as the first line in your blast2go.loc file. + +Consult the Blast2GO documentation for details about the property files and +setting up a local MySQL Blast2GO database. + + +History +======= + +v0.0.1 - Initial public release +v0.0.2 - Documentation clarifications, e.g. concatenated BLAST XML is allowed. + - Fixed error handler in wrapper script (for when b2g4pipe fails). + - Reformats the XML to use old NCBI-style concatenated BLAST XML since + b2g4pipe crashes with heap space error on with large files using + current NCBI output. +v0.0.3 - Include sample loc file, tool-data/blast2go.loc.sample +v0.0.4 - Include repository_dependencies.xml file for 'blastxml' format + (previously included in the core Galaxy installation) +v0.0.5 - Quote arguments in case of spaces in filenames (internal change) + - Last release supporting b2g4pipe v2.3.5 +v0.0.6 - Support for b2g4pipe v2.5 instead of v2.3.5 + - Now invoked with a class path and es.blast2go.prog.B2GAnnotPipe + rather then simply calling the jar file + - Now uses the switch -annot instead of -a (this change breaks + support for b2g4pipe v2.3.5 unfortunately) + - Catch a few error messages and treat them explicitly as errors. + + +Developers +========== + +This script and related tools are being developed on the following hg branch: +http://bitbucket.org/peterjc/galaxy-central/src/tools + +For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use +the following command from the Galaxy root folder: + +$ tar -czf blast2go.tar.gz tools/blast2go/blast2go.xml tools/blast2go/blast2go.py tools/blast2go/blast2go.txt tools/blast2go/repository_dependencies.xml tool-data/blast2go.loc.sample + +Check this worked: + +$ tar -tzf blast2go.tar.gz +tools/blast2go/blast2go.xml +tools/blast2go/blast2go.py +tools/blast2go/blast2go.txt +tools/blast2go/repository_dependencies.xml +tool-data/blast2go.loc.sample + + +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. + +NOTE: This is the licence for the Galaxy Wrapper only. Blast2GO and +associated data files are available and licenced separately. |
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| diff -r c8c04cd07ca0 -r e4419efbefad tools/blast2go/blast2go.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/blast2go/blast2go.xml Fri Feb 22 08:47:27 2013 -0500 |
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| @@ -0,0 +1,95 @@ +<tool id="blast2go" name="Blast2GO" version="0.0.6"> + <description>Maps BLAST results to GO annotation terms</description> + <command interpreter="python"> + blast2go.py "${xml}" "${prop.fields.path}" "${tab}" + </command> + <stdio> + <!-- Wrapper ensures anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <inputs> + <param name="xml" type="data" format="blastxml" label="BLAST XML results" description="You must have run BLAST against a protein database such as the NCBI non-redundant (NR) database. Use BLASTX for nucleotide queries, BLASTP for protein queries." /> + <param name="prop" type="select" label="Blast2GO settings" description="One or more configurations can be setup, such as using the Blast2GO team's server in Spain, or a local database."> + <options from_file="blast2go.loc"> + <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="path" index="2"/> + </options> + </param> + </inputs> + <outputs> + <data name="tab" format="tabular" label="Blast2GO ${prop.fields.name}" /> + </outputs> + <requirements> + </requirements> + <tests> + </tests> + <help> +.. class:: warningmark + +**Note**. Blast2GO may take a substantial amount of time, especially if +running against the public server in Spain. For large input datasets it +is advisable to allow overnight processing, or consider subdividing. + +----- + +**What it does** + +This runs b2g4Pipe, the command line (no GUI) version of Blast2GO designed +for use in pipelines. + +It takes as input BLAST XML results against a protein database, typically +the NCBI non-redundant (NR) database. This tool will accept concatenated +BLAST XML files (although they are technically invalid XML), which is very +useful if you have sub-divided your protein FASTA files and run BLAST on +them in batches. + +The BLAST matches are used to assign Gene Ontology (GO) annotation terms +to each query sequence. + +The output from this tool is a tabular file containing three columns, with +the order taken from query order in the original BLAST XML file: + +====== ==================================== +Column Description +------ ------------------------------------ + 1 ID and description of query sequence + 2 GO term + 3 GO description +====== ==================================== + +Note that if no GO terms are assigned to a sequence (e.g. if it had no +BLAST matches), then it will not be present in the output file. + + +**Advanced Settings** + +Blast2GO has a properties setting file which includes which database +server to connect to (e.g. the public server in Valencia, Spain, or a +local server), as well as more advanced options such as thresholds and +evidence code weights. To change these settings, your Galaxy administrator +must create a new properties file, and add it to the drop down menu above. + + +**References** + +S. Götz et al. +High-throughput functional annotation and data mining with the Blast2GO suite. +Nucleic Acids Res. 36(10):3420–3435, 2008. +http://dx.doi.org/10.1093/nar/gkn176 + +A. Conesa and S. Götz. +Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics. +Int. J. Plant Genomics. 619832, 2008. +http://dx.doi.org/10.1155/2008/619832 + +A. Conesa et al. +Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. +Bioinformatics 21:3674-3676, 2005. +http://dx.doi.org/10.1093/bioinformatics/bti610 + +http://www.blast2go.org/ + + </help> +</tool> |
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| diff -r c8c04cd07ca0 -r e4419efbefad tools/blast2go/repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/blast2go/repository_dependencies.xml Fri Feb 22 08:47:27 2013 -0500 |
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| @@ -0,0 +1,5 @@ +<?xml version="1.0"?> +<repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format)."> +<!-- Revision 4:f9a7783ed7b6 on the main tool shed is v0.0.14 which added BLAST databases --> +<repository toolshed="http://toolshed.g2.bx.psu.edu" name="blast_datatypes" owner="devteam" changeset_revision="f9a7783ed7b6" /> +</repositories> |
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| diff -r c8c04cd07ca0 -r e4419efbefad tools/ncbi_blast_plus/blast2go.py --- a/tools/ncbi_blast_plus/blast2go.py Wed Feb 20 13:33:47 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,147 +0,0 @@ -#!/usr/bin/env python -"""Galaxy wrapper for Blast2GO for pipelines, b2g4pipe v2.3.5. - -This script takes exactly three command line arguments: - * Input BLAST XML filename - * Blast2GO properties filename (settings file) - * Output tabular filename - -Sadly b2g4pipe (at least v2.3.5 to v2.5.0) cannot cope with current -style large BLAST XML files (e.g. from BLAST 2.2.25+), so we reformat -these to avoid it crashing with a Java heap space OutOfMemoryError. - -As part of this reformatting, we check for BLASTP or BLASTX output -(otherwise raise an error), and print the query count. - -It then calls the Java command line tool, and moves the output file to -the location Galaxy is expecting, and removes the tempory XML file. -""" -import sys -import os -import subprocess - -#You may need to edit this to match your local setup, -blast2go_jar = "/opt/b2g4pipe/blast2go.jar" - - -def stop_err(msg, error_level=1): - """Print error message to stdout and quit with given error level.""" - sys.stderr.write("%s\n" % msg) - sys.exit(error_level) - -if len(sys.argv) != 4: - stop_err("Require three arguments: XML filename, properties filename, output tabular filename") - -xml_file, prop_file, tabular_file = sys.argv[1:] - -#We should have write access here: -tmp_xml_file = tabular_file + ".tmp.xml" - -if not os.path.isfile(xml_file): - stop_err("Input BLAST XML file not found: %s" % xml_file) - -if not os.path.isfile(prop_file): - stop_err("Blast2GO configuration file not found: %s" % prop_file) - -def prepare_xml(original_xml, mangled_xml): - """Reformat BLAST XML to suit Blast2GO. - - Blast2GO can't cope with 1000s of <Iteration> tags within a - single <BlastResult> tag, so instead split this into one - full XML record per interation (i.e. per query). This gives - a concatenated XML file mimicing old versions of BLAST. - - This also checks for BLASTP or BLASTX output, and outputs - the number of queries. Galaxy will show this as "info". - """ - in_handle = open(original_xml) - footer = " </BlastOutput_iterations>\n</BlastOutput>\n" - header = "" - while True: - line = in_handle.readline() - if not line: - #No hits? - stop_err("Problem with XML file?") - if line.strip() == "<Iteration>": - break - header += line - - if "<BlastOutput_program>blastx</BlastOutput_program>" in header: - print "BLASTX output identified" - elif "<BlastOutput_program>blastp</BlastOutput_program>" in header: - print "BLASTP output identified" - else: - in_handle.close() - stop_err("Expect BLASTP or BLASTX output") - - out_handle = open(mangled_xml, "w") - out_handle.write(header) - out_handle.write(line) - count = 1 - while True: - line = in_handle.readline() - if not line: - break - elif line.strip() == "<Iteration>": - #Insert footer/header - out_handle.write(footer) - out_handle.write(header) - count += 1 - out_handle.write(line) - - out_handle.close() - in_handle.close() - print "Input has %i queries" % count - - -def run(cmd): - #Avoid using shell=True when we call subprocess to ensure if the Python - #script is killed, so too is the child process. - try: - child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) - except Exception, err: - stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) - #Use .communicate as can get deadlocks with .wait(), - stdout, stderr = child.communicate() - return_code = child.returncode - if return_code: - cmd_str = " ".join(cmd) - if stderr and stdout: - stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr)) - else: - stop_err("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr)) - #For early diagnostics, - else: - print stdout - print stderr - -if not os.path.isfile(blast2go_jar): - stop_err("Blast2GO JAR file not found: %s" % blast2go_jar) - -prepare_xml(xml_file, tmp_xml_file) -#print "XML file prepared for Blast2GO" - -#We will have write access wherever the output should be, -#so we'll ask Blast2GO to use that as the stem for its output -#(it will append .annot to the filename) -cmd = ["java", "-jar", blast2go_jar, - "-in", tmp_xml_file, - "-prop", prop_file, - "-out", tabular_file, #Used as base name for output files - "-a", # Generate *.annot tabular file - #"-img", # Generate images, feature not in v2.3.5 - ] -#print " ".join(cmd) -run(cmd) - -#Remove the temp XML file -os.remove(tmp_xml_file) - -out_file = tabular_file + ".annot" -if not os.path.isfile(out_file): - stop_err("ERROR - No output annotation file from Blast2GO") - -#Move the output file where Galaxy expects it to be: -os.rename(out_file, tabular_file) - -print "Done" |
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| diff -r c8c04cd07ca0 -r e4419efbefad tools/ncbi_blast_plus/blast2go.txt --- a/tools/ncbi_blast_plus/blast2go.txt Wed Feb 20 13:33:47 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,143 +0,0 @@ -Galaxy wrapper for Blast2GO for pipelines, b2g4pipe -=================================================== - -This wrapper is copyright 2011 by Peter Cock, The James Hutton Institute -(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. -See the licence text below. - -This is a wrapper for the command line Java tool b2g4pipe v2.3.5, -Blast2GO for pipelines. See: - -S. Götz et al. -High-throughput functional annotation and data mining with the Blast2GO suite. -Nucleic Acids Res. 36(10):3420–3435, 2008. -http://dx.doi.org/10.1093/nar/gkn176 - -A. Conesa and S. Götz. -Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics. -Int. J. Plant Genomics. 619832, 2008. -http://dx.doi.org/10.1155/2008/619832 - -A. Conesa et al. -Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. -Bioinformatics 21:3674-3676, 2005. -http://dx.doi.org/10.1093/bioinformatics/bti610 - -http://www.blast2go.org/ - - - -Installation -============ - -The main dependency is b2g4pipe which must be installed manually. Also we -strongly recommend installing a local Blast2GO database as well (see the -intructions below about the blast2go.loc file). - -You can change the path by editing the definition near the start of the Python -script blast2go.py, but by default it expects the underlying tool to be here: - -/opt/b2g4pipe/blast2go.jar - - -Installation of the Galaxy wrapper should work automatically via the Galaxy -Tool Shed, including the dependency on 'blast_datatypes' for the 'blastxml' -file format definition. To install the wrapper manually, first install -'blast_datatypes', then copy or move the following files under the Galaxy -tools folder, e.g. in the tools/ncbi_blast_blast folder: - -* blast2go.xml (the Galaxy tool definition) -* blast2go.py (the Python wrapper script) -* blast2go.txt (this README file) - -For a manual installation of the wrapper you will also need to modify the -tools_conf.xml file to tell Galaxy to offer the tool. We suggest putting -it next to the NCBI BLAST+ wrappers. Just add the line: - -<tool file="ncbi_blast_plus/blast2go.xml" /> - -As part of setting up b2g4pipe you will need to setup one or more Blast2GO -property files which tell the tool which database to use etc. The example -b2gPipe.properties provided with b2g4pipe v2.3.5 is out of date, with the -latest server IP address and database name given on the Blast2GO website. -These files can be anywhere accessable to the Galaxy Unix user, we put them -under /opt/b2g4pipe with the JAR file etc. - -You must tell Galaxy about these Blast2GO property files so that they can be -offered to the user. Copy file blast2go.loc.sample to tool-data/blast2go.loc -under the Galaxy folder and edit this to match your installation. This must -be plain text, tab separated, with three columns: - -(1) ID for the setup, e.g. Spain_2010_May -(2) Description for the setup, e.g. Database in Spain (May 2010) -(3) Properties filename for the setup, e.g. /opt/b2g4pipe/Spain_2010_May.properties - -Avoid including "Blast2GO" in the description (column 2) as this text will be -included in the automatically assigned output dataset name. The blast2go.loc -file allows you to customise the database setup. If for example you have a local -Blast2GO server running (which we recommend for speed), and you want this to be -the default setting, include it as the first line in your blast2go.loc file. - -Consult the Blast2GO documentation for details about the property files and -setting up a local MySQL Blast2GO database. - - -History -======= - -v0.0.1 - Initial public release -v0.0.2 - Documentation clarifications, e.g. concatenated BLAST XML is allowed. - - Fixed error handler in wrapper script (for when b2g4pipe fails). - - Reformats the XML to use old NCBI-style concatenated BLAST XML since - b2g4pipe crashes with heap space error on with large files using - current NCBI output. -v0.0.3 - Include sample loc file, tool-data/blast2go.loc.sample -v0.0.4 - Include repository_dependencies.xml file for 'blastxml' format - (previously included in the core Galaxy installation) -v0.0.5 - Quote arguments in case of spaces in filenames (internal change) - - -Developers -========== - -This script and related tools are being developed on the following hg branch: -http://bitbucket.org/peterjc/galaxy-central/src/tools - -For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use -the following command from the Galaxy root folder: - -$ tar -czf blast2go.tar.gz tools/ncbi_blast_plus/blast2go.xml tools/ncbi_blast_plus/blast2go.py tools/ncbi_blast_plus/blast2go.txt tools/ncbi_blast_plus/repository_dependencies.xml tool-data/blast2go.loc.sample - -Check this worked: - -$ tar -tzf blast2go.tar.gz -tools/ncbi_blast_plus/blast2go.xml -tools/ncbi_blast_plus/blast2go.py -tools/ncbi_blast_plus/blast2go.txt -tools/ncbi_blast_plus/repository_dependencies.xml -tool-data/blast2go.loc.sample - - -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. - -NOTE: This is the licence for the Galaxy Wrapper only. Blast2GO and -associated data files are available and licenced separately. |
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| diff -r c8c04cd07ca0 -r e4419efbefad tools/ncbi_blast_plus/blast2go.xml --- a/tools/ncbi_blast_plus/blast2go.xml Wed Feb 20 13:33:47 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,90 +0,0 @@ -<tool id="blast2go" name="Blast2GO" version="0.0.5"> - <description>Maps BLAST results to GO annotation terms</description> - <command interpreter="python"> - blast2go.py "${xml}" "${prop.fields.path}" "${tab}" - </command> - <inputs> - <param name="xml" type="data" format="blastxml" label="BLAST XML results" description="You must have run BLAST against a protein database such as the NCBI non-redundant (NR) database. Use BLASTX for nucleotide queries, BLASTP for protein queries." /> - <param name="prop" type="select" label="Blast2GO settings" description="One or more configurations can be setup, such as using the Blast2GO team's server in Spain, or a local database."> - <options from_file="blast2go.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - </inputs> - <outputs> - <data name="tab" format="tabular" label="Blast2GO ${prop.fields.name}" /> - </outputs> - <requirements> - </requirements> - <tests> - </tests> - <help> -.. class:: warningmark - -**Note**. Blast2GO may take a substantial amount of time, especially if -running against the public server in Spain. For large input datasets it -is advisable to allow overnight processing, or consider subdividing. - ------ - -**What it does** - -This runs b2g4Pipe, the command line (no GUI) version of Blast2GO designed -for use in pipelines. - -It takes as input BLAST XML results against a protein database, typically -the NCBI non-redundant (NR) database. This tool will accept concatenated -BLAST XML files (although they are technically invalid XML), which is very -useful if you have sub-divided your protein FASTA files and run BLAST on -them in batches. - -The BLAST matches are used to assign Gene Ontology (GO) annotation terms -to each query sequence. - -The output from this tool is a tabular file containing three columns, with -the order taken from query order in the original BLAST XML file: - -====== ==================================== -Column Description ------- ------------------------------------ - 1 ID and description of query sequence - 2 GO term - 3 GO description -====== ==================================== - -Note that if no GO terms are assigned to a sequence (e.g. if it had no -BLAST matches), then it will not be present in the output file. - - -**Advanced Settings** - -Blast2GO has a properties setting file which includes which database -server to connect to (e.g. the public server in Valencia, Spain, or a -local server), as well as more advanced options such as thresholds and -evidence code weights. To change these settings, your Galaxy administrator -must create a new properties file, and add it to the drop down menu above. - - -**References** - -S. Götz et al. -High-throughput functional annotation and data mining with the Blast2GO suite. -Nucleic Acids Res. 36(10):3420–3435, 2008. -http://dx.doi.org/10.1093/nar/gkn176 - -A. Conesa and S. Götz. -Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics. -Int. J. Plant Genomics. 619832, 2008. -http://dx.doi.org/10.1155/2008/619832 - -A. Conesa et al. -Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. -Bioinformatics 21:3674-3676, 2005. -http://dx.doi.org/10.1093/bioinformatics/bti610 - -http://www.blast2go.org/ - - </help> -</tool> |
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| diff -r c8c04cd07ca0 -r e4419efbefad tools/ncbi_blast_plus/repository_dependencies.xml --- a/tools/ncbi_blast_plus/repository_dependencies.xml Wed Feb 20 13:33:47 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -<?xml version="1.0"?> -<repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format)."> -<!-- Revision 4:f9a7783ed7b6 on the main tool shed is v0.0.14 which added BLAST databases --> -<repository toolshed="http://toolshed.g2.bx.psu.edu" name="blast_datatypes" owner="devteam" changeset_revision="f9a7783ed7b6" /> -</repositories> |