[galaxy-dev] Different display ratio (Tools, Center History)
Hi, How is it possible to change the deafult display ratio in galaxy? (The ratio between the tools, center history) Thanks, Hagai ___ 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] Issue with viz of mapped data in Trackster
OK (I see now I have posted twice the same error from the log - silly of me, sorry). First this: yes, the permissions in the data library are set so that only I and one other person can access the data library (set by one sharing role for both of us) The entries in the job table related to the summary tree converter: -- select * from job where tool_id like 'CONVERTER%summary_tree%' order by id desc; -- id |create_time |update_time | history_id | tool_id| tool_version | state | info | command_line | param_filename | runner_name | stdout | stderr | traceback | s ession_id | job_runner_name | job_runner_external_id | library_folder_id | user_id | imported | object_store_id | params | handler | exit_code --++++--+--+---+--- +-- --- ---++-+ +---+---+-- --+-++---+-+--+-++--+--- 8186 | 2013-03-19 09:22:29.165135 | 2013-03-19 09:27:44.335526 |622 | CONVERTER_bam_to_summary_tree_0 | 1.0.0 | ok| | python /home/galaxy/galaxy-dist/lib/galaxy/datatypes/converte rs/sam_or_bam_to_summary_tree_converter.py --bam /mnt/galaxydb/files/010/dataset_10477.dat /mnt/galaxydb/files/_metadata_files/001/metadata_1481.dat /m nt/galaxydb/files/013/dataset_13752.dat || | | | | 6188 | local:/// | 25218 | | 1 | f| || handler3 | 0 8185 | 2013-03-19 09:22:19.463602 | 2013-03-19 09:22:23.644461 |622 | CONVERTER_bam_to_summary_tree_0 | 1.0.0 | new | | || | | | | 6188 | local:/// | | | 1 | f | || handler2 | 8184 | 2013-03-19 09:20:45.225881 | 2013-03-19 09:26:54.337624 |622 | CONVERTER_bam_to_summary_tree_0 | 1.0.0 | ok| | python /home/galaxy/galaxy-dist/lib/galaxy/datatypes/converte rs/sam_or_bam_to_summary_tree_converter.py --bam /mnt/galaxydb/files/010/dataset_10461.dat /mnt/galaxydb/files/_metadata_files/001/metadata_1478.dat /m nt/galaxydb/files/013/dataset_13749.dat || | | | | 6188 | local:/// | 25112 | | 1 | f| || handler1 | 0 8183 | 2013-03-19 09:20:44.865602 | 2013-03-19 09:27:19.370773 |622 | CONVERTER_bam_to_summary_tree_0 | 1.0.0 | ok| | python /home/galaxy/galaxy-dist/lib/galaxy/datatypes/converte rs/sam_or_bam_to_summary_tree_converter.py --bam /mnt/galaxydb/files/010/dataset_10461.dat /mnt/galaxydb/files/_metadata_files/001/metadata_1477.dat /m nt/galaxydb/files/013/dataset_13750.dat || | | | | 6188 | local:/// | 25113 | | 1 | f| || handler1 | 0 8163 | 2013-03-19 08:29:59.965262 | 2013-03-19 08:34:30.257029 |622 | CONVERTER_bam_to_summary_tree_0 | 1.0.0 | ok| | python /home/galaxy/galaxy-dist/lib/galaxy/datatypes/converte rs/sam_or_bam_to_summary_tree_converter.py --bam /mnt/galaxydb/files/010/dataset_10457.dat /mnt/galaxydb/files/_metadata_files/001/metadata_1475.dat /m nt/galaxydb/files/013/dataset_13719.dat Thanks, Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 03/19/2013 10:54 PM, Jeremy Goecks wrote: Indeed, following error occurs: 157.193.10.150 - - [19/Mar/2013:08:30:06 +0200] GET /visualization/trackster HTTP/1.1 200 - http://galaxy.bits.vib.be/; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.22+ (KHTML, like Gecko) Chromium/17.0.963.56 Chrome/17.0.963.56 Safari/535.22+ galaxy.webapps.galaxy.api.datasets ERROR 2013-03-19 08:30:13,722 Error in dataset API at listing contents: : Traceback (most recent call last): File /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py, line 41, in show is_true( kwd.get( 'retry', False ) ) ) File /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py, line 96, in _converted_datasets_state if not data_provider.has_data( chrom ): File
Re: [galaxy-dev] show urls in csv (in eye mode)
Hi,
I found that in order to change static/scripts/mvc/data.js, I had to delete
static/scripts/packed/mvc/data.js.
After doing so, I have added the following patch in order to add links
inside tabular view.
else if (column_types[index] === 'str' || column_types === 'list') {
/* Left align all str columns, right align the rest */
-return $('td').addClass('stringalign').text(cell_contents);
+ var temp =
$('td').addClass('stringalign').text(cell_contents);
+ var text = Linkify(temp.text());
+ return temp.html(text);
}
I think this is better from the security aspect.
Now it looks like this:
chr147474796734088968.2326.21
http://genome.ucsc.edu/cgi-bin/hgTracks?db=m9position=chr1:4747-4119http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9position=chr1:4770447-4781119
chr149984769194991695.9322.77
http://genome.ucsc.edu/cgi-bin/hgTracks?db=m9position=chr1:4798-4316http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9position=chr1:4792498-4803416
I hope this might be useful for others as well.
Hagai
On Mon, Mar 18, 2013 at 6:14 PM, Hagai Cohen haga...@gmail.com wrote:
Hi,
I want to do this using a function which converts each URL into an html
link ( after the .text() was called).
(For example to use: https://github.com/maranomynet/linkify).
But now the galaxy code is a bit different and I can't find where should I
change the code.
I have found the _renderCell function here: static/scripts/mvc/data.js,
but I didn't succeed in changing it to add links to the html.
What am I doing wrong?
Thanks,
Hagai
On Sun, Feb 3, 2013 at 1:06 PM, Hagai Cohen haga...@gmail.com wrote:
Right.
I will convert it to text, allowing only simple links (a with href
only) to be shown.
Thanks,
Hagai
On Wed, Jan 30, 2013 at 8:03 PM, James Taylor ja...@jamestaylor.orgwrote:
You may want to be careful with this solution because it allows script
injection, any HTML including javascript in the uploaded tabular file
will be executed by the .html call, with complete access to everything
in the Galaxy browser window (like your session cookies).
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Jan 29, 2013 at 7:18 AM, Hagai Cohen haga...@gmail.com wrote:
Hi,
I found a simple solution.
In the file:
templates/dataset/tabular_chunked.mako
inside the method: renderCell - replace all jQuery .text(..) calls with
.html(..) calls.
Note:
Any entry in the csv with html syntax will be shown like html (links,
tags.
etc).
On Tue, Jan 29, 2013 at 1:39 PM, Hagai Cohen haga...@gmail.com
wrote:
Hi,
I have a tool which outputs a csv file with links.
When I press the eye icon - I would like these links to be shown as
links
in the browser.
It is possible?
Thanks,
Hagai
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Re: [galaxy-dev] Displaying track into UCSC (update)
Hello Carl, We are using galaxy-dist on revision a4113cc1cb5e. When we talk about private dataset, we mean datasets that have been uploaded to a user history through the Upload file tool. The access permission is allowed only to the current user role for these datasets. Anonymous user are not allowed on our galaxy instance. Regards, Julien Le 19 mars 2013 à 22:45, Carl Eberhard carlfeberh...@gmail.commailto:carlfeberh...@gmail.com a écrit : Hello, Stephanie and Julien What revision are you using IGBMC? Can you clarify what you mean by a private dataset? Are non-owners importing into a history via a shared history, or are they being passed a direct link to the UCSC display viewer from the owner? Thanks for the information, Carl On Tue, Mar 19, 2013 at 1:27 PM, Stephanie LE GRAS sleg...@igbmc.frmailto:sleg...@igbmc.fr wrote: Hi all, Here is an update regarding the problem we are facing with Julien with our local instance of Galaxy. As Julien said we are encountering a problem when trying to use UCSC display application on private dataset. UCSC is giving us the following error message : Unrecognized format line 2 of http://.../galaxy.bed (note: chrom names are case sensitive) We have worked for hours on it today and we have identified that datasets that can be uploaded to UCSC are actually public datasets and that Julien can upload all his datasets to UCSC because they are all public by default. What is interesting now is that we've seen that the path to the data in the UCSC error message is : http://www.galaxy-igbmc.fr/display_application/f1cb3a6ff6a93c01/ucsc_interv al_as_bed/main/bea5029fce8b957e/data/galaxy.bedhttp://www.galaxy-igbmc.fr/display_application/f1cb3a6ff6a93c01/ucsc_interval_as_bed/main/bea5029fce8b957e/data/galaxy.bed: While it should be : http://www.galaxy-igbmc.fr/display_at(Š)/galaxy.bedhttp://www.galaxy-igbmc.fr/display_at(%C5%A0)/galaxy.bed Because the right function to use in order to check whether the dataset can be uploaded to UCSC should be display_at but not display_application. Any ideas of what could cause Galaxy not to use the right function? Thank you in advance, Stephanie -- Stephanie Le Gras Bioinformatics engineer High throughput sequencing platform IGBMC 1, rue Laurent Fries 67404 ILLKIRCH Cedex France Tel. : +33 (0)3 88 65 32 73tel:%2B33%20%280%293%2088%2065%2032%2073 Tel. Solexa : +33 (0)3 88 65 32 97tel:%2B33%20%280%293%2088%2065%2032%2097 Le 18/03/13 19:20, « Julien SEILER » seil...@igbmc.frmailto:seil...@igbmc.fr a écrit : Hi all, We have installed a local galaxy server and we are encountering a problem when trying to use UCSC display application on private dataset. UCSC is giving us the following error message : Unrecognized format line 2 of http://.../galaxy.bed (note: chrom names are case sensitive) Curiously, it works fine with my personal account but it doesn't for all other users. It also works for displaying tracks based on a public dataset for all users. Could anybody explain us what's happening ? Thanks in advance for any help, Julien ___ 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/ ___ 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] Problem running ncbi_makeblastdb as real user in cluster
Il giorno mar, 19/03/2013 alle 15.20 -0400, Raj Ayyampalayam ha scritto: One of the first few tools I tested was the ncbi makebkastdb tool. When I try to run it the history for that particular job is immediately shown as follows: 0: (unnamed dataset) Failed to retrieve dataset information. An error occurred with this dataset:/hasattr(): attribute name must be string/ Hi Raj, this error in the history should be fixed by this patch: https://bitbucket.org/nsoranzo/peterjc-galaxy-central-tools2/commits/35163cbc6c694f598ed1a1875353c58b275e2423 I have sent a pull request to Peter (the maintainer), hopefully he will release soon a new version of blast_datatypes with this fix. Best, Nicola ___ 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] Problem running ncbi_makeblastdb as real user in cluster
On Wed, Mar 20, 2013 at 10:08 AM, Nicola Soranzo sora...@crs4.it wrote: Il giorno mar, 19/03/2013 alle 15.20 -0400, Raj Ayyampalayam ha scritto: One of the first few tools I tested was the ncbi makebkastdb tool. When I try to run it the history for that particular job is immediately shown as follows: 0: (unnamed dataset) Failed to retrieve dataset information. An error occurred with this dataset:/hasattr(): attribute name must be string/ Hi Raj, this error in the history should be fixed by this patch: https://bitbucket.org/nsoranzo/peterjc-galaxy-central-tools2/commits/35163cbc6c694f598ed1a1875353c58b275e2423 I have sent a pull request to Peter (the maintainer), hopefully he will release soon a new version of blast_datatypes with this fix. Best, Nicola The patch just removes the MetadataElement call - is that wise? Looking at the code, I don't see a recent API change regarding the name: https://bitbucket.org/galaxy/galaxy-central/history-node/default/lib/galaxy/datatypes/metadata.py?at=default Is there perhaps a universe_wsgi.ini setting which might be involved, since I've not seen this error locally? 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] Problem running ncbi_makeblastdb as real user in cluster
Il giorno mer, 20/03/2013 alle 12.41 +, Peter Cock ha scritto:
On Wed, Mar 20, 2013 at 10:08 AM, Nicola Soranzo sora...@crs4.it wrote:
Il giorno mar, 19/03/2013 alle 15.20 -0400, Raj Ayyampalayam ha
scritto:
One of the first few tools I tested was the ncbi makebkastdb tool. When
I try to run it the history for that particular job is immediately shown
as follows:
0: (unnamed dataset)
Failed to retrieve dataset information.
An error occurred with this dataset:/hasattr(): attribute name must be
string/
Hi Raj,
this error in the history should be fixed by this patch:
https://bitbucket.org/nsoranzo/peterjc-galaxy-central-tools2/commits/35163cbc6c694f598ed1a1875353c58b275e2423
I have sent a pull request to Peter (the maintainer), hopefully he will
release soon a new version of blast_datatypes with this fix.
Best,
Nicola
The patch just removes the MetadataElement call - is that wise?
Hi Peter,
my question instead is, what are they for? With 'name' they have no
meaning.
Looking at the code, I don't see a recent API change regarding
the name:
https://bitbucket.org/galaxy/galaxy-central/history-node/default/lib/galaxy/datatypes/metadata.py?at=default
Is there perhaps a universe_wsgi.ini setting which might be involved,
since I've not seen this error locally?
$ cd lib/galaxy/datatypes/
$ grep 'MetadataElement(' *.py|grep -v name
returns nothing, so the 'name' parameter is really mandatory.
Best,
Nicola
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Re: [galaxy-dev] customtrack visualisation
Hi Shaun. Is this still an issue for you this morning, on the public Main Galaxy server at https://main.g2.bx.psu.edu/? I am unable to reproduce with a test dataset: - bed custom track - datatype = customtrack - database = hg18 display at UCSC main is functional, and it is the only external display (this is expected). If you want to share a history with me, please send a link and note the dataset with the problem. Thanks, Jen Galaxy team On 3/19/13 2:44 AM, Shaun Webb wrote: Hi, I have lost my view in UCSC link on my customtrack datatypes, I'm not sure when this happened. External display links are still working ok for other datatypes. I have set the genome database to hg18. Any idea what I will need to edit to get this back? Thanks Shaun webb -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ 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] Some problems setting up a new cloudman instance on AWS
If anyone is following this thread, it turned out to be an error specific to Safari Web browser. The tool shed functionality works fine on Firefox. It has been identified as an issue and reproduced by the Galaxy team. Thanks Dannon for going above and beyond in tracking this down! Adam ___ 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] Problem running ncbi_makeblastdb as real user in cluster
On Wed, Mar 20, 2013 at 1:55 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Wed, Mar 20, 2013 at 1:52 PM, Nicola Soranzo sora...@crs4.it wrote:
Il giorno mer, 20/03/2013 alle 12.41 +, Peter Cock ha scritto:
The patch just removes the MetadataElement call - is that wise?
Hi Peter,
my question instead is, what are they for? With 'name' they have no
meaning.
Looking at the code, I don't see a recent API change regarding
the name:
https://bitbucket.org/galaxy/galaxy-central/history-node/default/lib/galaxy/datatypes/metadata.py?at=default
Is there perhaps a universe_wsgi.ini setting which might be involved,
since I've not seen this error locally?
$ cd lib/galaxy/datatypes/
$ grep 'MetadataElement(' *.py|grep -v name
returns nothing, so the 'name' parameter is really mandatory.
Best,
Nicola
Good question - I'd have to ask Edward what he thought this did,
but you seem to be right that as the code stands this metadata
element is rather pointless.
(I'm still puzzled why we don't see the error here though).
I'll apply your patch and test it locally...
Peter
Nicola - It looks good here, uploaded to the ToolShed as v0.0.15
http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
Raj - Could you apply the update from the ToolShed and
confirm if that fixes the problem for you?
Edward - have you received my direct email off list?
Thanks,
Peter
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[galaxy-dev] What are wrappers, how can I use this?
Hi, I installed galaxy locally and want to develop some tools, but I don't know where start. I would know what are wrappers and what I could do with this, and if is possible develop a tool in java. Thanks Ramão ___ 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] What are wrappers, how can I use this?
Sure, tools can be written in anything you'd like -- the wrapper you're referring to is just XML that tells galaxy how to interact with your command line tool. Here are some resources that should get you started: http://screencast.g2.bx.psu.edu/toolIntegration/ http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax -Dannon On Wed, Mar 20, 2013 at 11:11 AM, Ramon Tiburski ramao_tiago_tibur...@hotmail.com wrote: Hi, I installed galaxy locally and want to develop some tools, but I don't know where start. I would know what are wrappers and what I could do with this, and if is possible develop a tool in java. Thanks Ramão ___ 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] What are wrappers, how can I use this?
Thank you Dannon Date: Wed, 20 Mar 2013 11:17:19 -0400 Subject: Re: [galaxy-dev] What are wrappers, how can I use this? From: dannon.ba...@gmail.com To: ramao_tiago_tibur...@hotmail.com CC: galaxy-dev@lists.bx.psu.edu Sure, tools can be written in anything you'd like -- the wrapper you're referring to is just XML that tells galaxy how to interact with your command line tool. Here are some resources that should get you started: http://screencast.g2.bx.psu.edu/toolIntegration/ http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax -Dannon On Wed, Mar 20, 2013 at 11:11 AM, Ramon Tiburski ramao_tiago_tibur...@hotmail.com wrote: Hi, I installed galaxy locally and want to develop some tools, but I don't know where start. I would know what are wrappers and what I could do with this, and if is possible develop a tool in java. Thanks Ramão ___ 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] Problem running ncbi_makeblastdb as real user in cluster
Hi Guys,
Thanks for the quick response. I installed the latest blast datatypes
from the toolshed and that fixed the issue.
Peter, can you also fix the $outfile.extra_files_path to
$outfile.files_path on line 5 in the makedb wrapper xml file.
Thanks,
-Raj
On Wednesday, March 20, 2013 10:42:43 AM, Peter Cock wrote:
On Wed, Mar 20, 2013 at 1:55 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Wed, Mar 20, 2013 at 1:52 PM, Nicola Soranzo sora...@crs4.it wrote:
Il giorno mer, 20/03/2013 alle 12.41 +, Peter Cock ha scritto:
The patch just removes the MetadataElement call - is that wise?
Hi Peter,
my question instead is, what are they for? With 'name' they have no
meaning.
Looking at the code, I don't see a recent API change regarding
the name:
https://bitbucket.org/galaxy/galaxy-central/history-node/default/lib/galaxy/datatypes/metadata.py?at=default
Is there perhaps a universe_wsgi.ini setting which might be involved,
since I've not seen this error locally?
$ cd lib/galaxy/datatypes/
$ grep 'MetadataElement(' *.py|grep -v name
returns nothing, so the 'name' parameter is really mandatory.
Best,
Nicola
Good question - I'd have to ask Edward what he thought this did,
but you seem to be right that as the code stands this metadata
element is rather pointless.
(I'm still puzzled why we don't see the error here though).
I'll apply your patch and test it locally...
Peter
Nicola - It looks good here, uploaded to the ToolShed as v0.0.15
http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
Raj - Could you apply the update from the ToolShed and
confirm if that fixes the problem for you?
Edward - have you received my direct email off list?
Thanks,
Peter
--
Bio-informatics consultant
QBCG (http://qbcg.uga.edu)
706-542-6092
706-583-0442
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Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster
On Wed, Mar 20, 2013 at 3:43 PM, Raj Ayyampalayam ra...@uga.edu wrote: Hi Guys, Thanks for the quick response. I installed the latest blast datatypes from the toolshed and that fixed the issue. Great - thanks for letting us know so promptly. Peter, can you also fix the $outfile.extra_files_path to $outfile.files_path on line 5 in the makedb wrapper xml file. What do you mean 'fix' it? It should be using extra_files_path shouldn't it? This is a composite datatype in Galaxy. 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] Running jobs as real user and extra_file_path
On Mon, Apr 30, 2012 at 4:47 PM, Nate Coraor n...@bx.psu.edu wrote: On Apr 25, 2012, at 9:39 AM, Louise-Amélie Schmitt wrote: Hi everyone, I just wanted to ask how the extra_file_path is handled in case of job running as the real user since the file_path is only writable by the galaxy user. Any clue? Hi L-A, There are actually two dataset attributes for accessing the extra files directory, 'files_path' and 'extra_files_path'. 'extra_files_path' always points to the real path under the directory specified in the config file's 'file_path' option and should be used when providing a dataset's extra files directory as the input to a tool. 'files_path' points at the location that should be written to when used in a job so that the job's finish method can find the output files. This will be under the job_working_directory and thus writable by the actual user. So any tool outputs that use the extra files directory should use the output's 'files_path' attribute. Sorry for this confusion. There was talk some time ago about merging both attributes to work correctly in all cases, but this was never done. --nate Is this still the case? I'm guessing this is what Raj was alluding to with the BLAST+ wrapper for makeblastdb which creates a composite datatype as its output: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-March/013887.html If I'm using a single Linux/Unix galaxy user this doens't matter does it? 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] Problem running ncbi_makeblastdb as real user in cluster
On Wed, Mar 20, 2013 at 3:47 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Mar 20, 2013 at 3:43 PM, Raj Ayyampalayam ra...@uga.edu wrote: Hi Guys, Thanks for the quick response. I installed the latest blast datatypes from the toolshed and that fixed the issue. Great - thanks for letting us know so promptly. Peter, can you also fix the $outfile.extra_files_path to $outfile.files_path on line 5 in the makedb wrapper xml file. What do you mean 'fix' it? It should be using extra_files_path shouldn't it? This is a composite datatype in Galaxy. Are you perhaps running jobs as real user? That might explain when this difference is important: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-April/009579.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-March/013889.html 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] customtrack visualisation
Hi Jen, I should have said this is in my own install. It works fine at the main server. I only noticed this as I was running a tutorial I created last year. So I can only say that something has changed in the last year.. I was wondering where in the configuration files or scripts galaxy is told to provide this link for this type of dataset, perhaps there is something I need to reconfigure. Thanks Shaun Quoting Jennifer Jackson j...@bx.psu.edu on Wed, 20 Mar 2013 07:08:13 -0700: Hi Shaun. Is this still an issue for you this morning, on the public Main Galaxy server at https://main.g2.bx.psu.edu/? I am unable to reproduce with a test dataset: - bed custom track - datatype = customtrack - database = hg18 display at UCSC main is functional, and it is the only external display (this is expected). If you want to share a history with me, please send a link and note the dataset with the problem. Thanks, Jen Galaxy team On 3/19/13 2:44 AM, Shaun Webb wrote: Hi, I have lost my view in UCSC link on my customtrack datatypes, I'm not sure when this happened. External display links are still working ok for other datatypes. I have set the genome database to hg18. Any idea what I will need to edit to get this back? Thanks Shaun webb -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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] Problems with rsync from datacache.g2.bx.psu.edu/indexes
Hi Nate, I am trying to rsync the indexes and getting a rsync error. $ rsync -avz rsync://datacache.g2.bx.psu.edu/indexes/phiX . @ERROR: chroot failed rsync error: error starting client-server protocol (code 5) at main.c(1530) [receiver=3.0.6] Should I change anything in my command? Thanks, -Raj On 2/15/2013 11:22 AM, Nate Coraor wrote: On Feb 15, 2013, at 11:12 AM, Rodolfo Aramayo wrote: Hi, I hope this is the right place to ask, I am trying to rsync from: rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/ and I am getting the error: @ERROR: chroot failed rsync error: error starting client-server protocol (code 5) at main.c(1534) [Receiver=3.0.9 I know I can rsync to any other places Do you happen to know what is going on? Hi Rodolfo, The array on which the data cache is located is currently down due to an upgrade problem. We hope to have this fixed today. Sorry for the inconvenience. --nate Thanks --Rodolfo ___ 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/ -- Bio-informatics consultant QBCG (http://qbcg.uga.edu) 706-542-6092 706-583-0442 ___ 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] Cloudman on openstack
Hi, any update for cloudman with openstack . the page seems quite old http://wiki.galaxyproject.org/CloudMan/OpenStack -- Regards Zeeshan Ali Shah System Administrator - PDC HPC PhD researcher (IT security) Kungliga Tekniska Hogskolan +46 8 790 9115 http://www.pdc.kth.se/members/zashah ___ 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/
