3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9da922576dbf/ changeset: 9da922576dbf branch: split_blast2 user: peterjc date: 2012-04-13 16:07:12 summary: Correct comment in NCBI BLAST+ wrappers affected #: 5 files diff -r f6e790d9428273e2775b3e428c1fdd5f946a0ca3 -r 9da922576dbff75d9a432537ad07261435002563 tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -1,6 +1,6 @@ <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.11"><description>Search nucleotide database with nucleotide query sequence(s)</description> - <!-- If job splitting is enabled, break up the query file into batches of 500 sequences --> + <!-- If job splitting is enabled, break up the query file into four --><parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism><version_command>blastn -version</version_command><command interpreter="python">hide_stderr.py diff -r f6e790d9428273e2775b3e428c1fdd5f946a0ca3 -r 9da922576dbff75d9a432537ad07261435002563 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -1,6 +1,6 @@ <tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.11"><description>Search protein database with protein query sequence(s)</description> - <!-- If job splitting is enabled, break up the query file into batches of 500 sequences --> + <!-- If job splitting is enabled, break up the query file into four --><parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism><version_command>blastp -version</version_command><command interpreter="python">hide_stderr.py diff -r f6e790d9428273e2775b3e428c1fdd5f946a0ca3 -r 9da922576dbff75d9a432537ad07261435002563 tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -1,6 +1,6 @@ <tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.11"><description>Search protein database with translated nucleotide query sequence(s)</description> - <!-- If job splitting is enabled, break up the query file into batches of 500 sequences --> + <!-- If job splitting is enabled, break up the query file into four --><parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism><version_command>blastx -version</version_command><command interpreter="python">hide_stderr.py diff -r f6e790d9428273e2775b3e428c1fdd5f946a0ca3 -r 9da922576dbff75d9a432537ad07261435002563 tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -1,6 +1,6 @@ <tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.11"><description>Search translated nucleotide database with protein query sequence(s)</description> - <!-- If job splitting is enabled, break up the query file into batches of 500 sequences --> + <!-- If job splitting is enabled, break up the query file into four --><parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism><version_command>tblastn -version</version_command><command interpreter="python">hide_stderr.py diff -r f6e790d9428273e2775b3e428c1fdd5f946a0ca3 -r 9da922576dbff75d9a432537ad07261435002563 tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -1,6 +1,6 @@ <tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.11"><description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> - <!-- If job splitting is enabled, break up the query file into batches of 500 sequences --> + <!-- If job splitting is enabled, break up the query file into four --><parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism><version_command>tblastx -version</version_command><command interpreter="python">hide_stderr.py https://bitbucket.org/galaxy/galaxy-central/changeset/3b6aa127a6fe/ changeset: 3b6aa127a6fe branch: split_blast2 user: peterjc date: 2012-04-17 14:48:51 summary: Update scripts/check_python.py (Python 2.4 not supported) affected #: 1 file diff -r 9da922576dbff75d9a432537ad07261435002563 -r 3b6aa127a6fe8b86d82e354259cd5fa284766718 scripts/check_python.py --- a/scripts/check_python.py +++ b/scripts/check_python.py @@ -1,14 +1,14 @@ import os, sys msg = """ERROR: Your Python version is: %s -Galaxy is currently supported on Python 2.4, 2.5 and 2.6. To run Galaxy, +Galaxy is currently supported on Python 2.5, 2.6 and 2.7. To run Galaxy, please download and install a supported version from python.org. If a supported version is installed but is not your default, getgalaxy.org contains instructions on how to force Galaxy to use a different version.""" % sys.version[:3] def check_python(): try: - assert sys.version_info[:2] >= ( 2, 4 ) and sys.version_info[:2] <= ( 2, 7 ) + assert sys.version_info[:2] >= ( 2, 5 ) and sys.version_info[:2] <= ( 2, 7 ) except AssertionError: print >>sys.stderr, msg raise https://bitbucket.org/galaxy/galaxy-central/changeset/22f545c0d412/ changeset: 22f545c0d412 branch: split_blast2 user: peterjc date: 2012-04-18 11:36:23 summary: Handle merging bad BLAST XML files better affected #: 1 file diff -r 3b6aa127a6fe8b86d82e354259cd5fa284766718 -r 22f545c0d4129fe563a85928615a4db169eeba80 lib/galaxy/datatypes/xml.py --- a/lib/galaxy/datatypes/xml.py +++ b/lib/galaxy/datatypes/xml.py @@ -104,13 +104,41 @@ for f in split_files: h = open(f) body = False - header = [] + header = h.readline() + if not header: + out.close() + h.close() + raise ValueError("BLAST XML file %s was empty" % f) + if header.strip() != '<?xml version="1.0"?>': + out.write(header) #for diagnosis + out.close() + h.close() + raise ValueError("%s is not an XML file!" % f) + line = h.readline() + header += line + if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">', + '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']: + out.write(header) #for diagnosis + out.close() + h.close() + raise ValueError("%s is not a BLAST XML file!" % f) while True: line = h.readline() - header.append(line) + if not line: + out.write(header) #for diagnosis + out.close() + h.close() + raise ValueError("BLAST XML file %s ended prematurely" % f) + header += line if "<Iteration>" in line: break - header = "".join(header) + if len(header) > 10000: + #Something has gone wrong, don't load too much into memory! + #Write what we have to the merged file for diagnostics + out.write(header) + out.close() + h.close() + raise ValueError("BLAST XML file %s has too long a header!" % f) if "<BlastOutput>" not in header: out.close() h.close() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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