[galaxy-dev] requirement of complete command in code file
Hi All, I am doing some changes in galaxy software . I need the complete command in code file .is it possible ? if it's possible,provide me the code for that . Reagrds shashi shekhar ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Need help with uploading a perl script in Galaxy local instance
Hi, Thanks! I have removed the white spaces. I am actually a beginner in Perl so kindly bear with me. However I have one doubt, could it be because of the usage of the redirection operator used in the usage of the perl script? Kindly let me know. Regards. On Mon, May 23, 2011 at 3:16 AM, Vipin TS vipin...@gmail.com wrote: Hi Jayant, Hi, I am trying to upload a Perl script into Galaxy however it gives me an error *TypeError: 'NoneType' object does not support item assignment*. It seems that there is a mismatch between the input and output arguments and the file formats specified. I would really be thankful if someone can help me with this. Thanks in advance. Attached is the perl script, the configuration file for the perl script and the global tool_conf.xml file. Could you please consider to remove the white-space from your tool configuration file *methylation-snp.xml *for ex: command interpreter=perlallsnp_modified.pl $input $output/command data name=output format=gff3 / etc. HTH, Vipin -- Regards, JAYANT KHOPALE ___ 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: http://lists.bx.psu.edu/ -- JAYANT KHOPALE ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Fwd: Your message to galaxy-dev awaits moderator approval
I have also been getting such messages and even saying there are too many re-bounces so your account is being disabled and I can not reactivate using the link sent in email On Sun, May 22, 2011 at 11:28 PM, shashi shekhar meshash...@gmail.comwrote: -- Forwarded message -- From: galaxy-dev-boun...@lists.bx.psu.edu Date: Mon, May 23, 2011 at 11:42 AM Subject: Your message to galaxy-dev awaits moderator approval To: meshash...@gmail.com Your mail to 'galaxy-dev' with the subject requirement of complete command in code file Is being held until the list moderator can review it for approval. The reason it is being held: Post by non-member to a members-only list Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: http://lists.bx.psu.edu/confirm/galaxy-dev/32ca9fa0742b2f4b3a3e5ad2f9c57f06783f8188 ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Load balanced configuration unable to access Admin - Manage jobs?
I have had good success in setting up a load balanced configuration with nginx except that I get the following error when accessing Admin - Manage jobs: This Galaxy instance is not configured to run jobs. If using multiple servers, please directly access the job running instance to manage jobs. When I access the runner instance directly at http://localhost:8079/admin/jobs, the browser just hangs with no response. A quick search of the wiki and the dev mailing list archive didn't turn up a solution, so any help would be appreciated. Thanks, Olen ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] egg install failure: docutils, GeneTrack
On Mon, May 16, 2011 at 8:59 PM, Spunde, Alex aspu...@illumina.com wrote: Same thing: [aspunde@ilmnhw-biolin10 galaxy-dist]$ python ./scripts/fetch_eggs.py Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.6-linux-x86_64-ucs2.egg Fetched http://eggs.g2.bx.psu.edu/GeneTrack/GeneTrack-2.0.0_beta_1_dev_48da9e998f0caf01c5be731e926f4b0481f658f0-py2.6.egg One or more of the python eggs necessary to run Galaxy couldn't be downloaded automatically. You can try building them by hand (all at once) with: python scripts/scramble.py Or individually: python scripts/scramble.py Babel python scripts/scramble.py docutils python scripts/scramble.py GeneTrack I had a similar issue which was down to the file permissions - sudo fixed it, and I redid the chown afterwards. Peter ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Filter data and cut column bugs
Dear Peter: Yes, that would help. But, you patches are definitely not unnoticed. We'll apply them (likely at the conference) and we are also in the process of devising a strategy for doing so quickly and consistently. See you on Tuesday. a. Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org On May 23, 2011, at 10:02 AM, Peter Cock wrote: However, for future reference would it help if I emailed the list in parallel with filing bugs? None of these issues individually are overly complicated, and the sooner they get looked at the more likely it is my patches will still apply cleanly. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Checkboxes/booleans in tools, again
Not everything works correctly with checkbox booleans, the bug a couple people and I reported long ago https://bitbucket.org/galaxy/galaxy-central/issue/393/cant-use-checkbox-boolean-with-conditional is still there. 2011/5/23 Peter Cock p.j.a.c...@googlemail.com 2011/5/23 Louise-Amélie Schmitt louise-amelie.schm...@embl.de: Hello, I know this is still not fully implemented and that there has already been a lot of messages on the topic, but I just would like to know if there's a way to make the checked attribute in the param tags have the required effect. It might help if you were more precise - what isn't working for you? Ideally there would be an issue already reported on this on bitbucket. https://bitbucket.org/galaxy/galaxy-central/issues?sort=-id As I recall, the checked attribute is working fine for boolean parameters: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Peter ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Filter data and cut column bugs
On Mon, May 23, 2011 at 3:09 PM, Anton Nekrutenko an...@bx.psu.edu wrote: Dear Peter: Yes, that would help. One possibility would be to have all new bugs CC'd to the dev mailing list? Not sure if everyone here would like that or not... But, you patches are definitely not unnoticed. We'll apply them (likely at the conference) and we are also in the process of devising a strategy for doing so quickly and consistently. That sounds good :) See you on Tuesday. a. Thanks, Peter ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Need help with uploading a perl script in Galaxy local instance
Ah right. Overlooked the shortcut EMPTY
Just not my way of doing it..
Alex
Van: Vipin TS [vipin...@gmail.com]
Verzonden: maandag 23 mei 2011 17:39
Aan: Bossers, Alex
CC: Jayant Khopale; galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] Need help with uploading a perl script in Galaxy
local instance
Hi Alex,
Indeed looking at the script it should be possible to use it as Vipin
indicated.
However, for xml validity I wouldn't use the 'naked' or signs but use gt;
instead.
Thanks for pointing it.
I am curious though on the script. Is it part of a larger script? Don't see any
ARGs being read from command line but maybe my lack of knowledge.. ;P
Alex
I think there is a standard-in present inside the subroutine, as follows:
sub process_diff {
while(defined ($diff_line = ))
.
}
regards, Vipin
___
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:
http://lists.bx.psu.edu/
[galaxy-dev] Appropriate place to ask questions about your NGLIMS for Galaxy
Hi, I'm a newbie when it comes to this kind of thing, so I was wondering whether you can tell me the most appropriate place to ask questions about making some modifications to your nglims extension for galaxy? Should they be posted to the normal galaxy development list? Should I ask you directly? Cheers, Scott. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] can't run galaxy as daemon on Mac
hi, I can run galaxy in foreground on a mac just fine. However galaxy won't run in daemon mode. galaxy main page doesn't load, and I get no errors. Thanks. -Sohail___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Uploading Binary Files into Galaxy
Hi All, Sorry for the delay, I have had a couple of other projects on the go. Still no good. I have made the data type unsniffable and added what I thought was the correct information. I have also added the extension (sfx) to the list of unsniffable binary formats in binary.py but it does not make a difference. Code is as follows: ./datatypes_conf.xml datatype extension=sfx type=galaxy.datatypes.binary:Sfx display_in_upload=true/ ./lib/galaxy/datatypes/binary.py class Sfx( Binary ): Kanga and uAssembler Suffix Array file_ext = sfx def __init__( self, **kwd ): Binary.__init__( self, **kwd ) def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = 'Suffix Array sfx' dataset.blurb = 'binary data' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' My gut feeling is that this is related to the fact that Galaxy wants to look in the file, but as soon as its opened, it can't recognise the characters and it reports The uploaded binary file contains inappropriate content. I thought the set_peek method I have above would override the one described in the Class Binary. I have tried adding a sniffer tag into datatypes_conf.xml, but I get the same result whether the sniffer tag is there or not. I am sure I have missed a step or piece of content but I have no idea what I am missing... Thanks again for your time, Darren Cullerne Computational Biology CSIRO Plant Industry x5042 +61 2 62465042 darren.culle...@csiro.aumailto:darren.culle...@csiro.au ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Problem fore getting tool Command in code file
Hi All, I need the tool command in code file and want to change the command . is there any way to change the command which is given under command tag . Reagrds shashi shekhar ___ 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: http://lists.bx.psu.edu/
