# HG changeset patch # User peterjc # Date 1485958827 18000 # Node ID 69ab4d862db2287735f286a8dbf6271ce963c980 # Parent 7e50c54e70e63359fe4d46af6a475b19ec17118f v0.0.17 Used cached URL, python style updates diff -r 7e50c54e70e6 -r 69ab4d862db2 tools/effectiveT3/README.rst --- a/tools/effectiveT3/README.rst Tue Oct 13 11:44:18 2015 -0400 +++ b/tools/effectiveT3/README.rst Wed Feb 01 09:20:27 2017 -0500 @@ -1,7 +1,7 @@ Galaxy wrapper for EffectiveT3 v1.0.1 ===================================== -This wrapper is copyright 2011-2015 by Peter Cock, The James Hutton Institute +This wrapper is copyright 2011-2017 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. @@ -94,6 +94,8 @@ - Includes new standard classification model v2.0.2 (Sep 2015) as the default entry in ``tool-data/effectiveT3.loc`` - Catch java exception, e.g. if Java too old for ``TTSS-STD-2.0.1.jar`` +v0.0.17 - Update tool dependency definition to use cached URL. + - Minor internal changes to Python script for error reporting & style. ======= ====================================================================== diff -r 7e50c54e70e6 -r 69ab4d862db2 tools/effectiveT3/effectiveT3.py --- a/tools/effectiveT3/effectiveT3.py Tue Oct 13 11:44:18 2015 -0400 +++ b/tools/effectiveT3/effectiveT3.py Wed Feb 01 09:20:27 2017 -0500 @@ -16,30 +16,26 @@ import subprocess # The Galaxy auto-install via tool_dependencies.xml will set this environment variable -effectiveT3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/") -effectiveT3_jar = os.path.join(effectiveT3_dir, "TTSS_GUI-1.0.1.jar") +effective_t3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/") +effective_t3_jar = os.path.join(effective_t3_dir, "TTSS_GUI-1.0.1.jar") if "-v" in sys.argv or "--version" in sys.argv: # TODO - Get version of the JAR file dynamically? - print("Wrapper v0.0.16, TTSS_GUI-1.0.1.jar") + print("Wrapper v0.0.17, TTSS_GUI-1.0.1.jar") sys.exit(0) -def sys_exit(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) != 5: - sys_exit("Require four arguments: model, threshold, input protein FASTA file & output tabular file") + sys.exit("Require four arguments: model, threshold, input protein FASTA file & output tabular file") model, threshold, fasta_file, tabular_file = sys.argv[1:] if not os.path.isfile(fasta_file): - sys_exit("Input FASTA file not found: %s" % fasta_file) + sys.exit("Input FASTA file not found: %s" % fasta_file) if threshold not in ["selective", "sensitive"] \ -and not threshold.startswith("cutoff="): - sys_exit("Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold) + and not threshold.startswith("cutoff="): + sys.exit("Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold) + def clean_tabular(raw_handle, out_handle): """Clean up Effective T3 output to make it tabular.""" @@ -48,65 +44,66 @@ errors = 0 for line in raw_handle: if not line or line.startswith("#") \ - or line.startswith("Id; Description; Score;"): + or line.startswith("Id; Description; Score;"): continue assert line.count(";") >= 3, repr(line) # Normally there will just be three semi-colons, however the # original FASTA file's ID or description might have had # semi-colons in it as well, hence the following hackery: try: - id_descr, score, effective = line.rstrip("\r\n").rsplit(";",2) + id_descr, score, effective = line.rstrip("\r\n").rsplit(";", 2) # Cope when there was no FASTA description if "; " not in id_descr and id_descr.endswith(";"): id = id_descr[:-1] descr = "" else: - id, descr = id_descr.split("; ",1) + id, descr = id_descr.split("; ", 1) except ValueError: - sys_exit("Problem parsing line:\n%s\n" % line) + sys.exit("Problem parsing line:\n%s\n" % line) parts = [s.strip() for s in [id, descr, score, effective]] out_handle.write("\t".join(parts) + "\n") count += 1 if float(score) < 0: - errors += 1 + errors += 1 if effective.lower() == "true": - positive += 1 + positive += 1 return count, positive, errors + 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: - sys_exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) + sys.exit("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 or stderr.startswith("Exception in thread"): - cmd_str= " ".join(cmd) # doesn't quote spaces etc + cmd_str = " ".join(cmd) # doesn't quote spaces etc if stderr and stdout: - sys_exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr)) + sys.exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr)) else: - sys_exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr)) + sys.exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr)) -if not os.path.isdir(effectiveT3_dir): - sys_exit("Effective T3 folder not found: %r" % effectiveT3_dir) +if not os.path.isdir(effective_t3_dir): + sys.exit("Effective T3 folder not found: %r" % effective_t3_dir) -if not os.path.isfile(effectiveT3_jar): - sys_exit("Effective T3 JAR file not found: %r" % effectiveT3_jar) +if not os.path.isfile(effective_t3_jar): + sys.exit("Effective T3 JAR file not found: %r" % effective_t3_jar) -if not os.path.isdir(os.path.join(effectiveT3_dir, "module")): - sys_exit("Effective T3 module folder not found: %r" % os.path.join(effectiveT3_dir, "module")) +if not os.path.isdir(os.path.join(effective_t3_dir, "module")): + sys.exit("Effective T3 module folder not found: %r" % os.path.join(effective_t3_dir, "module")) -effectiveT3_model = os.path.join(effectiveT3_dir, "module", model) -if not os.path.isfile(effectiveT3_model): +effective_t3_model = os.path.join(effective_t3_dir, "module", model) +if not os.path.isfile(effective_t3_model): sys.stderr.write("Contents of %r is %s\n" - % (os.path.join(effectiveT3_dir, "module"), - ", ".join(repr(p) for p in os.listdir(os.path.join(effectiveT3_dir, "module"))))) - sys.stderr.write("Main JAR was found: %r\n" % effectiveT3_jar) - sys_exit("Effective T3 model JAR file not found: %r" % effectiveT3_model) + % (os.path.join(effective_t3_dir, "module"), + ", ".join(repr(p) for p in os.listdir(os.path.join(effective_t3_dir, "module"))))) + sys.stderr.write("Main JAR was found: %r\n" % effective_t3_jar) + sys.exit("Effective T3 model JAR file not found: %r" % effective_t3_model) # We will have write access whereever the output should be, temp_file = os.path.abspath(tabular_file + ".tmp") @@ -115,7 +112,7 @@ tabular_file = os.path.abspath(tabular_file) fasta_file = os.path.abspath(fasta_file) -cmd = ["java", "-jar", effectiveT3_jar, +cmd = ["java", "-jar", effective_t3_jar, "-f", fasta_file, "-m", model, "-t", threshold, @@ -124,14 +121,14 @@ try: # Must run from directory above the module subfolder: - os.chdir(effectiveT3_dir) -except: - sys_exit("Could not change to Effective T3 folder: %s" % effectiveT3_dir) + os.chdir(effective_t3_dir) +except Exception: + sys.exit("Could not change to Effective T3 folder: %s" % effective_t3_dir) run(cmd) if not os.path.isfile(temp_file): - sys_exit("ERROR - No output file from Effective T3") + sys.exit("ERROR - No output file from Effective T3") out_handle = open(tabular_file, "w") out_handle.write("#ID\tDescription\tScore\tEffective\n") @@ -143,11 +140,11 @@ os.remove(temp_file) if errors: - print("%i sequences, %i positive, %i errors" - % (count, positive, errors)) + print("%i sequences, %i positive, %i errors" + % (count, positive, errors)) else: - print("%i/%i sequences positive" % (positive, count)) + print("%i/%i sequences positive" % (positive, count)) -if count and count==errors: - # Galaxy will still allow them to see the output file - sys_exit("All your sequences gave an error code") +if count and count == errors: + # Galaxy will still allow them to see the output file + sys.exit("All your sequences gave an error code") diff -r 7e50c54e70e6 -r 69ab4d862db2 tools/effectiveT3/effectiveT3.xml --- a/tools/effectiveT3/effectiveT3.xml Tue Oct 13 11:44:18 2015 -0400 +++ b/tools/effectiveT3/effectiveT3.xml Wed Feb 01 09:20:27 2017 -0500 @@ -1,4 +1,4 @@ - + Find bacterial effectors in protein sequences effectiveT3 diff -r 7e50c54e70e6 -r 69ab4d862db2 tools/effectiveT3/tool_dependencies.xml --- a/tools/effectiveT3/tool_dependencies.xml Tue Oct 13 11:44:18 2015 -0400 +++ b/tools/effectiveT3/tool_dependencies.xml Wed Feb 01 09:20:27 2017 -0500 @@ -4,17 +4,22 @@ - http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_GUI-1.0.1.jar + + https://depot.galaxyproject.org/software/TTSS_GUI/TTSS_GUI_1.0.1_src_all.jar TTSS_GUI-1.0.1.jar$INSTALL_DIR $INSTALL_DIR/module - http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_ANIMAL-1.0.1.jar + + https://depot.galaxyproject.org/software/TTSS_ANIMAL/TTSS_ANIMAL_1.0.1_src_all.jar TTSS_ANIMAL-1.0.1.jar$INSTALL_DIR/module/ - http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_PLANT-1.0.1.jar + + https://depot.galaxyproject.org/software/TTSS_PLANT/TTSS_PLANT_1.0.1_src_all.jar TTSS_PLANT-1.0.1.jar$INSTALL_DIR/module/ - http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_STD-1.0.1.jar + + https://depot.galaxyproject.org/software/TTSS_STD/TTSS_STD_1.0.1_src_all.jar TTSS_STD-1.0.1.jar$INSTALL_DIR/module/ - http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_STD-2.0.2.jar + + https://depot.galaxyproject.org/software/TTSS_STD/TTSS_STD_2.0.2_src_all.jar TTSS_STD-2.0.2.jar$INSTALL_DIR/module/