Mercurial > repos > earlhaminst > export_to_cluster
changeset 2:b97775e9fe06 draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit f5c5f3d6ce676937f5c673ec7fc0631a9f490dc2
| author | earlhaminst |
|---|---|
| date | Fri, 24 Mar 2017 12:20:48 -0400 |
| parents | a9d1991c90e3 |
| children | 9838eed606ad |
| files | export_to_cluster.py export_to_cluster.xml |
| diffstat | 2 files changed, 10 insertions(+), 8 deletions(-) [+] |
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--- a/export_to_cluster.py Mon Oct 03 06:26:41 2016 -0400 +++ b/export_to_cluster.py Fri Mar 24 12:20:48 2017 -0400 @@ -24,15 +24,16 @@ real_export_dir = os.path.realpath(options.export_dir) dir_prefix = options.dir_prefix.rstrip(os.sep) if not real_export_dir.startswith(dir_prefix): - sys.exit("%s must be a subdirectory of %s" % (options.export_dir, dir_prefix)) + raise Exception("%s must be a subdirectory of %s" % (options.export_dir, dir_prefix)) if not os.path.exists(real_export_dir): - sys.exit("%s does not exist or it is not accessible by the Galaxy user" % options.export_dir) + raise Exception("%s does not exist or it is not accessible by the Galaxy user" % options.export_dir) if not os.path.isdir(real_export_dir): - sys.exit("%s is not a directory" % options.export_dir) + raise Exception("%s is not a directory" % options.export_dir) dataset_paths = args[::3] dataset_names = args[1::3] dataset_exts = args[2::3] +exit_code = 0 for dp, dn, de in zip(dataset_paths, dataset_names, dataset_exts): """ Copied from get_valid_filename from django @@ -46,5 +47,6 @@ print("Dataset '%s' copied to '%s'" % (dn, dest)) except Exception as e: msg = "Error copying dataset '%s' to '%s', %s" % (dn, dest, e) - print(msg) - sys.stderr.write(msg) + print(msg, file=sys.stderr) + exit_code = 1 +sys.exit(exit_code)
--- a/export_to_cluster.xml Mon Oct 03 06:26:41 2016 -0400 +++ b/export_to_cluster.xml Fri Mar 24 12:20:48 2017 -0400 @@ -2,13 +2,13 @@ <requirements> <requirement type="set_environment">EXPORT_DIR_PREFIX</requirement> </requirements> - <command> + <command detect_errors="aggressive"> <![CDATA[ -python $__tool_directory__/export_to_cluster.py -d '$export_dir' -p "\$EXPORT_DIR_PREFIX" +python '$__tool_directory__/export_to_cluster.py' -d '$export_dir' -p "\$EXPORT_DIR_PREFIX" #for $d in $datasets '${d}' '${d.hid}: ${d.name}' '${d.ext}' #end for -> $log +> '$log' ]]> </command> <inputs>