Hi John,

Is all your semi-colon fixing on the trunk? I've found another bug in
this area (patch below), which is showing up with task splitting under
SGE.

e.g. this job is meant to be running and merging 5 BLAST XML files, stderr:

nothing to merge for
/mnt/galaxy/galaxy-central/database/files/000/dataset_498.dat
(expected 5 files)

/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_0:
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_0/galaxy_288_60.sh:
line 13: syntax error near unexpected token `;'
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_0/galaxy_288_60.sh:
line 13: `/mnt/galaxy/galaxy-central/extract_dataset_parts.sh
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_0;
blastn -query 
"/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_0/dataset_495.dat"
  -db "/mnt/scratch/local/blast/ncbi/nt" -task megablast -evalue 0.001
-out 
"/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_0/dataset_498.dat"
    -outfmt 5 -num_threads 8 -dust yes -strand both -max_target_seqs
3; return_code=$?; cd /mnt/galaxy/galaxy-central; ; sh -c "exit
$return_code"'
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_1:
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_1/galaxy_288_61.sh:
line 13: syntax error near unexpected token `;'
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_1/galaxy_288_61.sh:
line 13: `/mnt/galaxy/galaxy-central/extract_dataset_parts.sh
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_1;
blastn -query 
"/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_1/dataset_495.dat"
  -db "/mnt/scratch/local/blast/ncbi/nt" -task megablast -evalue 0.001
-out 
"/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_1/dataset_498.dat"
    -outfmt 5 -num_threads 8 -dust yes -strand both -max_target_seqs
3; return_code=$?; cd /mnt/galaxy/galaxy-central; ; sh -c "exit
$return_code"'
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_2:
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_2/galaxy_288_62.sh:
line 13: syntax error near unexpected token `;'
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_2/galaxy_288_62.sh:
line 13: `/mnt/galaxy/galaxy-central/extract_dataset_parts.sh
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_2;
blastn -query 
"/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_2/dataset_495.dat"
  -db "/mnt/scratch/local/blast/ncbi/nt" -task megablast -evalue 0.001
-out 
"/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_2/dataset_498.dat"
    -outfmt 5 -num_threads 8 -dust yes -strand both -max_target_seqs
3; return_code=$?; cd /mnt/galaxy/galaxy-central; ; sh -c "exit
$return_code"'
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_3:
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_3/galaxy_288_63.sh:
line 13: syntax error near unexpected token `;'
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_3/galaxy_288_63.sh:
line 13: `/mnt/galaxy/galaxy-central/extract_dataset_parts.sh
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_3;
blastn -query 
"/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_3/dataset_495.dat"
  -db "/mnt/scratch/local/blast/ncbi/nt" -task megablast -evalue 0.001
-out 
"/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_3/dataset_498.dat"
    -outfmt 5 -num_threads 8 -dust yes -strand both -max_target_seqs
3; return_code=$?; cd /mnt/galaxy/galaxy-central; ; sh -c "exit
$return_code"'
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_4:
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_4/galaxy_288_64.sh:
line 13: syntax error near unexpected token `;'
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_4/galaxy_288_64.sh:
line 13: `/mnt/galaxy/galaxy-central/extract_dataset_parts.sh
/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_4;
blastn -query 
"/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_4/dataset_495.dat"
  -db "/mnt/scratch/local/blast/ncbi/nt" -task megablast -evalue 0.001
-out 
"/mnt/galaxy/galaxy-central/database/job_working_directory/000/288/task_4/dataset_498.dat"
    -outfmt 5 -num_threads 8 -dust yes -strand both -max_target_seqs
3; return_code=$?; cd /mnt/galaxy/galaxy-central; ; sh -c "exit
$return_code"'

Note the repeated semi-colon, which causes the child jobs to fail (patch below).

There is however a second bug, the merge fails yet the history entry
is still green (success). The merge method is raising a ValueError yet
it is being ignored.

Regards,

Peter

$ hg branch
default

$ hg tip
changeset:   12028:8e001dc9675c
tag:         tip
user:        John Chilton <jmchil...@gmail.com>
date:        Wed Oct 16 23:15:21 2013 -0500
summary:     Dependencies: Do not attempt to install package
dependencies in tool shed if the will be ignored.

$ hg diff lib/galaxy/jobs/command_factory.py
diff -r 8e001dc9675c lib/galaxy/jobs/command_factory.py
--- a/lib/galaxy/jobs/command_factory.py    Wed Oct 16 23:15:21 2013 -0500
+++ b/lib/galaxy/jobs/command_factory.py    Thu Oct 17 10:50:18 2013 +0100
@@ -58,7 +58,7 @@
         if not captured_return_code:
             commands += capture_return_code_command
             captured_return_code = True
-        commands += "; cd %s; " % abspath( getcwd() )
+        commands += "; cd %s " % abspath( getcwd() )
         commands += job_wrapper.setup_external_metadata(
             exec_dir=abspath( getcwd() ),
             tmp_dir=job_wrapper.working_directory,
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