changeset 9:887adf823bc0 draft

v0.0.10 - Python 3 compatiblity etc (overdue upload)

--- a/tools/blast2go/README.rst	Thu Mar 26 11:15:22 2015 -0400
+++ b/tools/blast2go/README.rst	Tue Dec 06 16:26:16 2022 +0000
@@ -1,7 +1,7 @@
 Galaxy wrapper for Blast2GO for pipelines, b2g4pipe
 ===================================================
 
-This wrapper is copyright 2011-2014 by Peter Cock, The James Hutton Institute
+This wrapper is copyright 2011-2015 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below (MIT licence).
 
@@ -16,8 +16,10 @@
 http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go
 
 
-References
-==========
+Citation
+========
+
+Please cite the following papers:
 
 Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
 Galaxy tools and workflows for sequence analysis with applications
@@ -46,8 +48,8 @@
 ======================
 
 Installation via the Galaxy Tool Shed should take care of the Galaxy side of
-things, including the dependency on 'blast_datatypes' which defines the
-'blastxml' file format. However, you will also probably need to configure
+things, including the dependency on ``blast_datatypes`` which defines the
+``blastxml`` file format. However, you will also probably need to configure
 the Blast2GO property file(s), for example if you have a local Blast2GO
 database (which we recommend for speed).
 
@@ -62,30 +64,30 @@
 
 * http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip
 
-You can change the path by setting the B2G4PIPE environement variable to
+You can change the path by setting the ``$B2G4PIPE`` environment variable to
 the desired folder, but by default the script looks for the JAR file here::
 
     /opt/b2g4pipe_v2.5/blast2go.jar
 
-To install the wrapper manually, first install 'blast_datatypes', then
+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:
+``tools/blast2go/`` folder:
 
-* blast2go.xml (the Galaxy tool definition)
-* blast2go.py (the Python wrapper script)
-* massage_xml_for_blast2go.py (Python XML reformatting script)
-* README.rst (this file)
+- ``blast2go.xml`` (the Galaxy tool definition)
+- ``blast2go.py`` (the Python wrapper script)
+- ``massage_xml_for_blast2go.py`` (Python BLAST XML reformatting script)
+- ``README.rst`` (this 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
+``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" />
 
-If you wish to run the unit tests, also add this to tools_conf.xml.sample
-and move/copy the test-data files under Galaxy's test-data folder. Then::
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
 
-    $ ./run_functional_tests.sh -id blast2go
+    $ ./run_tests.sh -id blast2go
 
 
 Configuration
@@ -162,6 +164,8 @@
           of the Blast2GO command line tool. For now b2g4pipe v2.5 is still
           available as a free download.
         - Tool definition now embeds citation information.
+v0.0.10 - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================
 
 
@@ -175,23 +179,33 @@
 As of September 2013, development is continuing on a dedicated GitHub repository:
 https://github.com/peterjc/galaxy_blast
 
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
-the following command from the Galaxy root folder::
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+Planemo commands (which requires you have set your Tool Shed access details in
+``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
 
-    $ tar -czf blast2go.tar.gz tools/blast2go/README.rst tools/blast2go/blast2go.xml tools/blast2go/blast2go.py tools/blast2go/massage_xml_for_blast2go.py tools/blast2go/repository_dependencies.xml tools/blast2go/tool_dependencies.xml tool-data/blast2go.loc.sample test-data/blastp_sample.xml test-data/blastp_sample.blast2go.tabular
+    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blast2go/
+    ...
+
+or::
+
+    $ planemo shed_update -t toolshed --check_diff ~/repositories/galaxy_blast/tools/blast2go/
+    ...
 
-Check this worked::
+To just build and check the tar ball, use::
 
-    $ tar -tzf blast2go.tar.gz
+    $ planemo shed_upload --tar_only  ~/repositories/galaxy_blast/tools/blast2go/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/blastp_sample.blast2go.tabular
+    test-data/blastp_sample.xml
+    tool-data/blast2go.loc.sample
     tools/blast2go/README.rst
+    tools/blast2go/blast2go.py
     tools/blast2go/blast2go.xml
-    tools/blast2go/blast2go.py
     tools/blast2go/massage_xml_for_blast2go.py
     tools/blast2go/repository_dependencies.xml
     tools/blast2go/tool_dependencies.xml
-    tool-data/blast2go.loc.sample
-    test-data/blastp_sample.xml
-    test-data/blastp_sample.blast2go.tabular
+
 
 
 Licence (MIT)

--- a/tools/blast2go/blast2go.py	Thu Mar 26 11:15:22 2015 -0400
+++ b/tools/blast2go/blast2go.py	Tue Dec 06 16:26:16 2022 +0000
@@ -30,57 +30,52 @@
 import os
 import subprocess
 
-#You may need to edit this to match your local setup,
+# You may need to edit this to match your local setup,
 blast2go_dir = os.environ.get("B2G4PIPE", "/opt/b2g4pipe_v2.5/")
 blast2go_jar = os.path.join(blast2go_dir, "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)
 
 try:
     from massage_xml_for_blast2go import prepare_xml
 except ImportError:
-    stop_err("Missing sister file massage_xml_for_blast2go.py")
+    sys.exit("Missing sister file massage_xml_for_blast2go.py")
 
 if len(sys.argv) != 4:
-    stop_err("Require three arguments: XML filename, properties filename, output tabular filename")
+    sys.exit("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:
+# 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)
+    sys.exit("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)
+    sys.exit("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
+        # 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)
+        sys.exit("Blast2GO configuration file not found: %s" % prop_file)
     del tmp
 
 
 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.
+    # 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(),
+        sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
     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
+    # 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:
@@ -90,14 +85,14 @@
     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:
+    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:
+    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)
+        sys.exit(error_msg)
 
 
 blast2go_classpath = os.path.split(blast2go_jar)[0]
@@ -105,30 +100,30 @@
 blast2go_classpath = "%s/*:%s/ext/*:" % (blast2go_classpath, blast2go_classpath)
 
 prepare_xml(xml_file, tmp_xml_file)
-#print "XML file prepared for Blast2GO"
+# 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)
+# 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
+       "-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)
+# print " ".join(cmd)
 run(cmd)
 
-#Remove the temp XML file
+# 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")
+    sys.exit("ERROR - No output annotation file from Blast2GO")
 
-#Move the output file where Galaxy expects it to be:
+# Move the output file where Galaxy expects it to be:
 os.rename(out_file, tabular_file)
 
 print "Done"

--- a/tools/blast2go/blast2go.xml	Thu Mar 26 11:15:22 2015 -0400
+++ b/tools/blast2go/blast2go.xml	Tue Dec 06 16:26:16 2022 +0000
@@ -1,16 +1,16 @@
-<tool id="blast2go" name="Blast2GO" version="0.0.9">
+<tool id="blast2go" name="Blast2GO" version="0.0.10">
     <description>Maps BLAST results to GO annotation terms</description>
     <requirements>
         <requirement type="package" version="2.5">b2g4pipe</requirement>
     </requirements>
-    <command interpreter="python">
-        blast2go.py "${xml}" "${prop.fields.path}" "${tab}"
-    </command>
     <stdio>
         <!-- Wrapper ensures anything other than zero is an error -->
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
+    <command interpreter="python">
+        blast2go.py "${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.">

--- a/tools/blast2go/massage_xml_for_blast2go.py	Thu Mar 26 11:15:22 2015 -0400
+++ b/tools/blast2go/massage_xml_for_blast2go.py	Tue Dec 06 16:26:16 2022 +0000
@@ -14,19 +14,14 @@
 
 This script is called from my Galaxy wrapper for Blast2GO for pipelines,
 available from the Galaxy Tool Shed here:
-http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go 
+http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go
 
 This script is under version control here:
 https://github.com/peterjc/galaxy_blast/tree/master/blast2go
 """
 import sys
 import os
-import subprocess
 
-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)
 
 def prepare_xml(original_xml, mangled_xml):
     """Reformat BLAST XML to suit Blast2GO.
@@ -45,19 +40,19 @@
     while True:
         line = in_handle.readline()
         if not line:
-            #No hits?
-            stop_err("Problem with XML file?")
+            # No hits?
+            sys.exit("Problem with XML file?")
         if line.strip() == "<Iteration>":
             break
         header += line
 
     if "<BlastOutput_program>blastx</BlastOutput_program>" in header:
-        print "BLASTX output identified"
+        print("BLASTX output identified")
     elif "<BlastOutput_program>blastp</BlastOutput_program>" in header:
-        print "BLASTP output identified"
+        print("BLASTP output identified")
     else:
         in_handle.close()
-        stop_err("Expect BLASTP or BLASTX output")
+        sys.exit("Expect BLASTP or BLASTX output")
 
     out_handle = open(mangled_xml, "w")
     out_handle.write(header)
@@ -68,25 +63,25 @@
         if not line:
             break
         elif line.strip() == "<Iteration>":
-           #Insert footer/header
-           out_handle.write(footer)
-           out_handle.write(header)
-           count += 1
+            # 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
+    print("Input has %i queries" % count)
 
 
 if __name__ == "__main__":
     # Run the conversion...
     if len(sys.argv) != 3:
-        stop_err("Require two arguments: XML input filename, XML output filename")
+        sys.exit("Require two arguments: XML input filename, XML output filename")
 
     xml_file, out_xml_file = sys.argv[1:]
 
     if not os.path.isfile(xml_file):
-        stop_err("Input BLAST XML file not found: %s" % xml_file)
+        sys.exit("Input BLAST XML file not found: %s" % xml_file)
 
     prepare_xml(xml_file, out_xml_file)

--- a/tools/blast2go/repository_dependencies.xml	Thu Mar 26 11:15:22 2015 -0400
+++ b/tools/blast2go/repository_dependencies.xml	Tue Dec 06 16:26:16 2022 +0000
@@ -1,4 +1,4 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <repositories description="Requires BLAST XML and database datatype definitions.">
-    <repository changeset_revision="5482a8cd0f36" name="blast_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
-</repositories>
+    <repository name="blast_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="01b38f20197e"/>
+</repositories>
\ No newline at end of file

--- a/tools/blast2go/tool_dependencies.xml	Thu Mar 26 11:15:22 2015 -0400
+++ b/tools/blast2go/tool_dependencies.xml	Tue Dec 06 16:26:16 2022 +0000
@@ -9,13 +9,15 @@
 		<!-- Galaxy moves into the unzipped folder b2g4pipe -->
                 <action type="shell_command">
 cp b2gPipe.properties Spain_2012_August.properties &amp;&amp;
-sed -i "s/Dbacces.dbname=b2g_apr12/Dbacces.dbname=b2g_aug12/g" Spain_2012_August.properties &amp;&amp;
-sed -i "s/Dbacces.dbhost=10.10.100.203/Dbacces.dbhost=publicdb.blast2go.com/g" Spain_2012_August.properties
+sed -i.bak "s/Dbacces.dbname=b2g_apr12/Dbacces.dbname=b2g_aug12/g" Spain_2012_August.properties &amp;&amp;
+sed -i.bak "s/Dbacces.dbhost=10.10.100.203/Dbacces.dbhost=publicdb.blast2go.com/g" Spain_2012_August.properties
+rm Spain_2012_August.properties.bak
                 </action>
                 <action type="shell_command">
 cp b2gPipe.properties Spain_2011_June.properties &amp;&amp;
-sed -i "s/Dbacces.dbname=b2g_apr12/Dbacces.dbname=b2g_jun11/g" Spain_2011_June.properties &amp;&amp;
-sed -i "s/Dbacces.dbhost=10.10.100.203/Dbacces.dbhost=publicdb.blast2go.com/g" Spain_2011_June.properties
+sed -i.bak "s/Dbacces.dbname=b2g_apr12/Dbacces.dbname=b2g_jun11/g" Spain_2011_June.properties &amp;&amp;
+sed -i.bak "s/Dbacces.dbhost=10.10.100.203/Dbacces.dbhost=publicdb.blast2go.com/g" Spain_2011_June.properties
+rm Spain_2011_June.properties.bak
                 </action>
                 <action type="move_directory_files"><source_directory>.</source_directory><destination_directory>$INSTALL_DIR/</destination_directory></action>
                 <!-- Set environment variable $B2G4PIPE so Python script knows where to look -->