Patch for RepeatMasker.xml for RepeatMasker 3.3.0
Dear Galaxians, We are using Galaxy with RepeatMasker 3.3.0. I don't know whether that is the expected version, as I can't find any statement about what is required in the Galaxy tool dependencies for RepeatMasker. Anyway, when a job is submitted with no repeats, RepeatMasker 3.3.0 doesn't create the various output and summary files (.tbl, .out.gff, .out.html, .masked). This causes the Galaxy job to fail with an error message that scares the end user. I attach a patch to handle this case, by touch'ing these files before trying to copy them. Now such jobs succeed with empty output. I think this is clearer, and certainly less scary. Is there a better mechanism for me to contribute such fixes other than posting patches on this list? cheers, Simon ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================
On Jan 31, 2013, at 8:15 PM, Guest, Simon wrote:
Dear Galaxians,
We are using Galaxy with RepeatMasker 3.3.0. I don't know whether that is the expected version, as I can't find any statement about what is required in the Galaxy tool dependencies for RepeatMasker.
Anyway, when a job is submitted with no repeats, RepeatMasker 3.3.0 doesn't create the various output and summary files (.tbl, .out.gff, .out.html, .masked). This causes the Galaxy job to fail with an error message that scares the end user.
I attach a patch to handle this case, by touch'ing these files before trying to copy them. Now such jobs succeed with empty output. I think this is clearer, and certainly less scary.
Is there a better mechanism for me to contribute such fixes other than posting patches on this list?
This tool exists in the tool shed, and the best way to contribute to the patch is to contact the tool repository owner directly via email. As it happens, the tool author also frequents this list, so I've cc'd him and he may respond directly to your email. Tool shed features are planned to make this process easier in the future. Best, J.
Hi Simon, thank you for your contribution. I updated the toolshed version to 0.1.1 with your changes. Ciao! Bjoern
Dear Galaxians,
We are using Galaxy with RepeatMasker 3.3.0. I don't know whether that is the expected version, as I can't find any statement about what is required in the Galaxy tool dependencies for RepeatMasker.
Anyway, when a job is submitted with no repeats, RepeatMasker 3.3.0 doesn't create the various output and summary files (.tbl, .out.gff, .out.html, .masked). This causes the Galaxy job to fail with an error message that scares the end user.
I attach a patch to handle this case, by touch'ing these files before trying to copy them. Now such jobs succeed with empty output. I think this is clearer, and certainly less scary.
Is there a better mechanism for me to contribute such fixes other than posting patches on this list?
cheers, Simon
======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
-
Björn Grüning -
Guest, Simon -
Jeremy Goecks