[galaxy-dev] macs in galaxy
In running macs in galaxy, the following error was found ERROR:root:mfold format error! Your input is '32'. It should be like '10,30' A format for mfold like 10,30 is expected... but the default value configured in xml remains as 32. will there be an updated version of this xml in future? Also after altering the default display mfold value to 10,30, type integer in the param tag for mfold become erroneous. May I ask what is the correct type for input format 10,30? Thanks alot ___ 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] Issue with file permissions of uploaded files
Hi all, we have our own Galaxy server running under Nginx. Recently we changed the 'user' of Nginx in the Nginx configuration file from 'galaxy' to a more general 'www' since we plan to use Nginx for other purposes as well. Now the Get data - Upload file does not work any longer because of file permissions. Files are uploaded correctly to a directory /local/data/galaxy_tmp/upload_store/ but then are owned by the 'www' user and read-writeable by this other only. Thus, the Galaxy user 'galaxy' cannot open them, cannot determine the file type and the whole Upload file process fails. How can I set the file permissions of uploaded files? Do I need to enter a matching 'umask' in some Galaxy configuration or in some Nginx configuration file. Any links to where to set such a umask would be greatly appreciated. Thanks, Joern -- Joern Toedling, PhD Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de Tel.: +49 6131 39 21511 ___ 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] Failure to prepare job error
Hello, I'm running a Python/R tool from my Amazon Galaxy instance. To use R, I import a package I've installed called PypeR. My tool works fine from the command line, but when I try to run it on my Amazon instance, it gives me this error: Traceback (most recent call last): File /nfs/software/galaxy/lib/galaxy/jobs/runners/local.py, line 61, in run_job job_wrapper.prepare() File /nfs/software/galaxy/lib/galaxy/jobs/__init__.py, line 371, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /nfs/software/galaxy/lib/galaxy/tools/__init__.py, line 1543, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /nfs/software/galaxy/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /nfs/software/galaxy/eggs/Cheetah-2.2.2-py2.6-linux-i686-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File cheetah_DynamicallyCompiledCheetahTemplate_1311891781_86_41894.py, line 83, in respond EOFError: EOF when reading a line With the additional caption failure to prepare job. I've been struggling with this for days, and I'm pretty sure I don't have a typo in my .xml file. How can I solve this? Thanks, Rafi Torsten Schwab Marketing GmbH Emanuelstr. 3, 10317 Berlin Deutschland Telefon: +49 (33) 5310967 Email: woozyd...@gmail.com Site: http://flug.prexxis.de/ ___ 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] [API] Get the hashed dataset id within Galaxy
Thanks a lot! I found another way to do it but it is awfully more complicated so I'll change as soon as I have some time. Best, L-A Le 23/08/2011 19:49, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Hi, I would need to make a tool that can get the API dataset id out of the input dataset of the tool, how can I do that? Hi L-A, Pass in as an argument: $__app__.security.encode_id( 'file.%s' % $input1.id ) Where 'input1' is the param name of your input. --nate ___ 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] tool which using web service
hi, I have application , i want to integrate that application like ucsc_browser in my local instance of galaxy .Application create some input data ,that data i want to send into galaxy to process. can u help me how can i add such type of tool in Galaxy ? Regards shashi ___ 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] tool which using web service
Hello Sashi, Look at our tool wikis at http://wiki.g2.bx.psu.edu/Admin/Tools You probably want to base your tool config file on ~/tools/data-source/ucsc_tablebrowser.xml. Greg Von kuster On Aug 24, 2011, at 9:12 AM, shashi shekhar wrote: hi, I have application , i want to integrate that application like ucsc_browser in my local instance of galaxy .Application create some input data ,that data i want to send into galaxy to process. can u help me how can i add such type of tool in Galaxy ? Regards shashi ___ 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/ Greg Von Kuster Galaxy Development Team g...@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] Display BAM with IGV
Hi Nate,
I have been able to get this to work on a Mac and Windows XP within
limited guide lines. The following are what I had to do to make it work:
My Mac is now running Java 1.6.0_26, Firefox 3.6.20, Google Crome
ver.13.0.782.215 and Safari 5.1 (6534.50). In addition I have installed Max
OS 10.6.8 Supplemental Update 1.0. My PC is running Windows XP SP3 with
Java 1.6.0_26, Firefox 3.6.20 and IE8. Windows updates are at current
levels. I have not tested this on Windows 7.
I am currently able to run the IGV-web tool from Galaxy via Firefox, Crome
and Safari on the Mac and IE8 only on Windows. When I use either Firefox or
Crome on Windows I get the following error.
ERROR [2011-08-24 09:22:40,169] [TrackLoader.java:211]
[SwingWorker-pool-20352093-thread-1] java.lang.RuntimeException:
java.lang.RuntimeException: Error loading file:
http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908
0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length
ERROR [2011-08-24 09:22:40,169] [TrackManager.java:245]
[SwingWorker-pool-20352093-thread-1] Error loading tracks
org.broad.igv.exceptions.DataLoadException: htmlAn error occurred while
loading:
http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908
0aa/data/galaxy_afa21414c9c9e7eb.bambrjava.lang.RuntimeException: Error
loading file:
http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908
0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length
at org.broad.igv.track.TrackLoader.load(TrackLoader.java:212)
at org.broad.igv.track.TrackManager.load(TrackManager.java:271)
at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241)
at
org.broad.igv.ui.IGVMainFrame$StartupWorker.doInBackground(IGVMainFrame.java
:2775)
at com.jidesoft.utils.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at com.jidesoft.utils.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown
Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
This error appears to be different from the original, at least in
details though the results are the same. I am also going to post this with
IGV support.
Thanks,
Iry
On 8/15/11 2:46 PM, Nate Coraor n...@bx.psu.edu wrote:
Iry Witham wrote:
Hi Nate,
I have checked the nginx.conf file and they comply to the documentation:
# added to allow nginx to handle file downloads
location /_x_accel_redirect/ {
internal;
alias /;
I have also confirmed that the universe_wsgi.ini file contains the
following:
And the following to the [app:main] section of universe_wsgi.ini:
nginx_x_accel_redirect_base = /_x_accel_redirect
Iry
This will need some in-depth debugging, then.
If you access Galaxy directly via the port of its built-in web server
(by default, 8080), and request to display a dataset, does it set the
X-Accel-Redirect header in the response?
If you access the same dataset via the nginx address but rename the
underlying disk file, do you get an error message from nginx or from
Galaxy?
--nate
On 8/15/11 10:46 AM, Nate Coraor n...@bx.psu.edu wrote:
Iry Witham wrote:
Hi Everyone,
I have been tasked with getting the IGV working within our Galaxy
instance. I have modified our Nginx configuration based on the more
advanced
configuration under Sending files using nginx on the nginxProxy page in
the
wiki. The IGV viewer component in Galaxy does not display the results from
a
BAM file in either the web or local instance of IGV. I have tested with
IGV1.5 and with version 2.03. Neither produce a visual representation of
the
sequence. When attempting to use the web option we get the same error
provided in the original post as noted below. Has anyone gotten this to
work
with Nginx-0.8.53 or any of the newer versions?
Hi Iry,
Have you checked to make sure that your nginx server is serving the file
for download, as opposed to the internal Galaxy web server? In the
original email, it looked like nginx was being bypassed entirely (due to
serving on port 8080 - Galaxy's intenal server's default port). But
even once nginx is in use, it's necessary to set up X-Accel-Redirect to
serve datasets. See the instructions here:
http://usegalaxy.org/production
--nate
Thanks,
Iry Witham
Applications Administrator
Scientific Computing Group
Computational Sciences Dept.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609
Phone: 207-288-6744
email: iry.wit...@jax.org
On Apr 27, 2011; 10:06am
³Hello all,
I just updated our local copy of Galaxy and just wanted to try the new IGV
display application.
When I try to display a BAM file with the local IGV or the
[galaxy-dev] LDAP NGINX
Dear all, I'd like to integrate external user authentication with our local galaxy installation. So far we are running nginx as proxy, but all examples I found for LDAP and galaxy are for apache. Is anybody out there who has a working installation with LDAP and nginx? Cheers, Holger -- Dr. Holger Klein Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de/ Tel: +49(6131) 39 21511 ___ 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] Installing local instance hiccup
Hello, I am in the process of installing a local instance, and I can't seem to be able to build the bx_python egg, even with scramble.py. Any ideas to get around this? Cheers, Steve - Dr Stephen R. Doyle Postdoctoral Researcher Genetics Department | La Trobe University | Bundoora 3086 Australia T: +61 3 9479 3087 | F: +61 3 9479 2480 | E: s.do...@latrobe.edu.aumailto:s.do...@latrobe.edu.au | W: http://www.latrobe.edu.au/genetics/staff/stephen_doyle.htm La Trobe University - ranked top in Victoria for student satisfaction (Sweeney Uni Student Report, 2009) CRICOS Provider 00115M J Please kindly consider your environment before printing this e-mail Warning to recipients: This email and any attachments are confidential and subject to copyright. If you are not the intended recipient any use, disclosure or copying is unauthorised. If you have received this email in error please advise us immediately by reply email and delete all copies. It is your responsibility to examine this email and any attachments for viruses. Any personal information in this email must be handled in accordance with the Information Privacy Act 2000 (Vic). ___ 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] macs in galaxy
Hi Jayce, Are you running this on your local instance? It seems you are running MACS 1.4, which our wrapper does not support yet, but we are planning to add a wrapper for 1.4 soon. Thanks, K On Wed, Aug 24, 2011 at 4:20 AM, KOH Jia Yu Jayce ko...@gis.a-star.edu.sgwrote: In running macs in galaxy, the following error was found ERROR:root:mfold format error! Your input is '32'. It should be like '10,30' A format for mfold like 10,30 is expected… but the default value configured in xml remains as 32. will there be an updated version of this xml in future? Also after altering the default display mfold value to 10,30, type integer in the param tag for mfold become erroneous. May I ask what is the correct type for input format 10,30? Thanks alot ___ 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] Installing local instance hiccup
Hi Stephen, What platform are you running on? Thanks, K On Wed, Aug 24, 2011 at 3:53 AM, Stephen Doyle s.do...@latrobe.edu.auwrote: Hello, I am in the process of installing a local instance, and I can't seem to be able to build the bx_python egg, even with scramble.py. Any ideas to get around this? Cheers, Steve - Dr Stephen R. Doyle Postdoctoral Researcher Genetics Department | La Trobe University | Bundoora 3086 Australia T: +61 3 9479 3087 | F: +61 3 9479 2480 | E: s.do...@latrobe.edu.au | W: http://www.latrobe.edu.au/genetics/staff/stephen_doyle.htm *La Trobe University - ranked top in Victoria for student satisfaction (Sweeney Uni Student Report, 2009) * CRICOS Provider 00115M J Please kindly consider your environment before printing this e-mail Warning to recipients: This email and any attachments are confidential and subject to copyright. If you are not the intended recipient any use, disclosure or copying is unauthorised. If you have received this email in error please advise us immediately by reply email and delete all copies. It is your responsibility to examine this email and any attachments for viruses. Any personal information in this email must be handled in accordance with the Information Privacy Act 2000 (Vic). ___ 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] tool which using web service
i have an application ,from there i want input file in galaxy like usc_browser. in tools/data-source/ucsc_tablebrowser.xml u are passing some values from galaxy to ucsc_browser .and theen u are getting some info from ucsc browser. i want to crate tool like this. can i get any documents for such type of tool. thanks for reply On Wed, Aug 24, 2011 at 6:57 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Sashi, Look at our tool wikis at http://wiki.g2.bx.psu.edu/Admin/Tools You probably want to base your tool config file on ~/tools/data-source/ucsc_tablebrowser.xml. Greg Von kuster On Aug 24, 2011, at 9:12 AM, shashi shekhar wrote: hi, I have application , i want to integrate that application like ucsc_browser in my local instance of galaxy .Application create some input data ,that data i want to send into galaxy to process. can u help me how can i add such type of tool in Galaxy ? Regards shashi ___ 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/ Greg Von Kuster Galaxy Development Team g...@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] Error when using build_profile_indexes.py on hg19
Hi Sarah, Sorry for the late reply. The error is related to a bug we're currently looking into. If you run it again, does it have this error consistently or does it only happen once in a while? Thanks, K On Thu, Jul 7, 2011 at 12:11 PM, Sarah Diehl di...@immunbio.mpg.de wrote: Hi everybody, when I run the build_profile_indexes.py script in the scripts/tools/annotation_**profiler/ directory on hg19 (downloaded yesterday from UCSC), I get the following error: Created table dir (profiled_annotations/hg19/** wgEncodeOpenChromFaireGlioblaB**aseOverlapSignal). ['fileName'] Table wgEncodeOpenChromFaireGlioblaB**aseOverlapSignal (/galaxy/galaxy_data/ucsc_**data/hg19/**wgEncodeOpenChromFaireGlioblaB**aseOverlapSignal.sql) does not appear to have a chromosome, a start, or a stop. Removing empty table (**wgEncodeOpenChromFaireGlioblaB**aseOverlapSignal) directory (profiled_annotations/hg19/**wgEncodeOpenChromFaireGlioblaB** aseOverlapSignal). Created table dir (profiled_annotations/hg19/** wgEncodeCshlShortRnaSeqK562Chr**omatinShortTransfrags). ['bin', 'chrom', 'chromStart', 'chromEnd', 'name', 'score', 'strand', 'length', 'numUnique', 'numReads', 'minSeqCount', 'maxSeqCount', 'aveSeqCount', 'firstSeqCount', 'medSeqCount', 'thirdSeqCount', 'minReadCount', 'maxReadCount', 'aveReadCount', 'firstReadCount', 'medReadCount', 'thirdReadCount', 'numRegions', 'regStart', 'regLength', 'seqCount', 'regCount', 'sumCount', 'KEY', 'KEY'] Traceback (most recent call last): File /galaxy/galaxy_backup/galaxy-**dist/scripts/tools/annotation_** profiler/build_profile_**indexes.py, line 338, in module if __name__ == __main__: __main__() File /galaxy/galaxy_backup/galaxy-**dist/scripts/tools/annotation_** profiler/build_profile_**indexes.py, line 310, in __main__ bitset_dict[ chrom ].set_range( start, end - start ) File bitset.pyx, line 128, in bx.bitset.BitSet.set_range (lib/bx/bitset.c:1130) File bitset.pyx, line 93, in bx.bitset.b_check_range_count (lib/bx/bitset.c:656) IndexError: End 16573 is larger than the size of this BitSet (16571). Everything worked fine with mm9 and dm3. Since the script wasn't changed in the last year, I suspect it has to do with the UCSC data. We don't really use hg19, so I'm fine with just leaving it out for now, but I wanted to report the error anyway. Best regards, Sarah __**_ 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] Launching a JAVA or external app
Hi Alex, Sorry for the late reply. Can you elaborate more on your needs? Does the Java app require filenames/params that can't be passed through the command line? Thanks, K On Mon, Jun 27, 2011 at 9:57 AM, Bossers, Alex alex.boss...@wur.nl wrote: Hello all, would it be possible to launch for instance a JAVA app with preloaded parameters and files from galaxy that needs interaction/display? For instance a gui based annotation editor? It necessarily doesn't have to support saving of files back to galaxy. Sort of end stage. Any help or pointers appreciated. thanks Alex ___ 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] Sam2interval.py bug
Hi Shaun, Thanks for reporting this, I have just committed the fix. I will let you know if we add the read_name to the truncated output. -K On Tue, Aug 2, 2011 at 6:54 AM, SHAUN WEBB swe...@staffmail.ed.ac.ukwrote: Hi, I've noticed a bug in sam2interval.py. There are a few indentation errors in the final lines of code. I think there should be an indent after: if not ref_name == '*': And this whole if statement should be included in the for loop above. Also, would you be able to add read_name to the truncated output (when not printing all fields). This makes downstream analysis a lot easier, e.g. looking at reads that map multiple times. Thanks Shaun Webb -- 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/ ___ 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] latest checkout (today) does not have Help or User
Joseph Hargitai wrote:
Hi,
built a new server today to test a few things.
a, Help is not clickable via Apache2 proxy
2, when you use an apache2 proxy is it for granted that local authentication
cannot be used? I tired
remote-user = False
hoping i can use load-balancing and proxy but retain local authentication.
But User remains unclickable.
Hi Joe,
Both Help and User are not direct links, but hovering over this text
should activate a popup menu. If this is not the case it's possible
that the appropriate javascript is not loading.
By local authentication, do you mean Galaxy's internal authentication,
or your site's local authentication system? You can use Galaxy behind a
proxy without using your site's authentication, even if Apache is
configured to authenticate users. By setting:
use_remote_user = False
(the default), Galaxy will ignore any authentication data (the
REMOTE_USER header) provided by Apache. If you are trying to do the
opposite (use your site's authentication in Apache to authenticate
Galaxy users), you'll need to set use_remote_user to True.
3, Using Nginx
anyone has a full nginx config script? The wiki has the snippets which I am
not sure where to fit in nginx nomenclature - does it go in conf or virtual
sites enabled.
The snippets include the block they go inside, so for example, the
first:
http {
# ... other http stuff ...
upstream galaxy_app {
server localhost:8080;
}
server {
client_max_body_size 10G;
# ... other server stuff ...
location / {
proxy_pass http://galaxy_app;
proxy_set_header X-Forwarded-Host $host;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
}
}
}
In this case, the 'upstream' block goes inside 'http'. 'server' goes
inside 'http' and contains the 'location' block.
I am assuming the local authentication can be done with nginx as is done on
the cloud version. Which would be the goal.
Yes, it can.
--nate
thanks,
joe
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Re: [galaxy-dev] value_label tool input param attribute doesn't work as documented
Hi Leandro,
I tested this on my instance and the example you gave did give me the
correct string: Human (hg18). Do you still have this problem? If so, can you
provide an example where it still behaves incorrectly?
Thanks,
K
On Thu, Jul 14, 2011 at 4:16 AM, Leandro Hermida soft...@leandrohermida.com
wrote:
Hi,
Looking at the example on the Tool Config Syntax wiki page:
Example
Assume that the tool includes an input parameter named database which is
a select list ( e.g., assume the following inputs ):
Toggle line
numbershttp://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#
1
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b4282c0f9aa2576fbdec6550c3174f_1
inputs
2
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b4282c0f9aa2576fbdec6550c3174f_2
param format=tabular name=input type=data label=Input stuff/
3
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b4282c0f9aa2576fbdec6550c3174f_3
param type=select name=database label=Database
4
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b4282c0f9aa2576fbdec6550c3174f_4
option value=alignseq.loc*Human (hg18)*/option
5
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b4282c0f9aa2576fbdec6550c3174f_5
option value=faseq.locFly (dm3)/option
6
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b4282c0f9aa2576fbdec6550c3174f_6
/param
7
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b4282c0f9aa2576fbdec6550c3174f_7
/inputs
Assume that the user selects the first option in the $database select
list. Then the following will ensure that the tool produces a tabular data
set whose associated history item has the label Blat on *Human (hg18)*.
Toggle line
numbershttp://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#
1
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-c1ccb05e35e84df1d17f7b92455ff66b9d18618b_1
outputs
2
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-c1ccb05e35e84df1d17f7b92455ff66b9d18618b_2
data format=input name=output label=Blat on
${database.value_label} /
3
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-c1ccb05e35e84df1d17f7b92455ff66b9d18618b_3
/outputs
It shows that .value_label attribute should produce the string in between
the option tags, not the actual value.
Why does this not work? When I use it it produces the value, or am I doing
something wrong?
regards,
Leandro
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Re: [galaxy-dev] Failure to prepare job error
Woozy wrote: Hello, I'm running a Python/R tool from my Amazon Galaxy instance. To use R, I import a package I've installed called PypeR. My tool works fine from the command line, but when I try to run it on my Amazon instance, it gives me this error: Traceback (most recent call last): File /nfs/software/galaxy/lib/galaxy/jobs/runners/local.py, line 61, in run_job job_wrapper.prepare() File /nfs/software/galaxy/lib/galaxy/jobs/__init__.py, line 371, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /nfs/software/galaxy/lib/galaxy/tools/__init__.py, line 1543, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /nfs/software/galaxy/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /nfs/software/galaxy/eggs/Cheetah-2.2.2-py2.6-linux-i686-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File cheetah_DynamicallyCompiledCheetahTemplate_1311891781_86_41894.py, line 83, in respond EOFError: EOF when reading a line With the additional caption failure to prepare job. I've been struggling with this for days, and I'm pretty sure I don't have a typo in my .xml file. How can I solve this? Hi Rafi, Could you post your tool configuration to the list? Thanks, --nate Thanks, Rafi Torsten Schwab Marketing GmbH Emanuelstr. 3, 10317 Berlin Deutschland Telefon: +49 (33) 5310967 Email: woozyd...@gmail.com Site: http://flug.prexxis.de/ ___ 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] checkboxes bug fix
Hi L-A, I tried this on today's tip but could not reproduce the bug. I added your param param name=SQA type=boolean label=Run SolexaQA checked=true / to a tool and the correct value was produced on the command line and in the configfiles block as well. Re-running also gave the correct result. Are you still seeing this problem? Thanks, K 2011/8/15 Louise-Amélie Schmitt louise-amelie.schm...@embl.de Hello, Sorry for being late, again, but please find the tool attached. Here is my last pull: 5743:720455407d1c Stuff changed in the file but in the end I had to make the same modification again (change true to false) since it didn't work anymore. Best, L-A Le 15/06/2011 09:56, Louise-Amélie Schmitt a écrit : Hi, and sorry for the late reply Here is the last pull: 5355:50e249442c5a I'll try to be as concise as I can but I can send you the whole file if you need it. It's not completely done yet though. This is a tool that produces a HTML file containing the results of various quality assessment programs. To trigger or block the execution of a specific program, I use checkboxes in the form, like this: param name=SQA type=boolean label=Run SolexaQA checked=true / Then, I use the configfile name=script tags to define a shell script that will be modified with cheetah tests on the checkboxes. Then the final script is sent to another shell script that will check its existence and launch it: command interpreter='sh'all_QA.sh $script /command As you can see, the checkboxes are checked by default. But before the change I mentioned is my last email, un-checking them didn't have any effect whatsoever. The following test, for instance, was always true: #if $SQA.value == True Moreover, even if I un-checked the checkboxes and ran the tool, then clicked the re-run button in the result in my history, all of them were checked in the form that appears, as if I never un-checked them. Now, the state of the checkboxes is respected and I can properly choose what to run in my tool. Hope that helps. L-A Le 08/06/2011 20:54, Jennifer Jackson a écrit : Hi L-A, Could you describe a use case (which tool/from, what options/input)? If you know the last pull # for your local install, that would also be helpful for us to know. Best, Jen Galaxy team On 6/6/11 2:15 AM, Louise-Amélie Schmitt wrote: Hi, Since I haven't updated Galaxy for a while now I don't know if it was actually fixed but I had issues with my default-selected checkboxes: When I deselected them, the value sent in the query remained as if they were still selected. Even when I re-ran the job, all the checkboxes were selected as if I never deselected them. Therefore, in lib/galaxy/web/form_builder.py I changed: 105 return 'input type=checkbox id=%s name=%s value=true%s%sinput type=hidden name=%s%s value=true%s' \ for: 105 return 'input type=checkbox id=%s name=%s value=true%s%sinput type=hidden name=%s%s value=false%s' \ And it works fine now :) Cheers, L-A __**_ 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] Issue with file permissions of uploaded files
You can also use the 'upload_store_access' option to the nginx upload module to make the files readable: http://www.grid.net.ru/nginx/upload.en.html --nate Kanwei Li wrote: Hi Joern, Would it be easier to just chmod the directories to reflect the new user? -K On Wed, Aug 24, 2011 at 4:42 AM, Joern Toedling j.toedl...@imb-mainz.dewrote: Hi all, we have our own Galaxy server running under Nginx. Recently we changed the 'user' of Nginx in the Nginx configuration file from 'galaxy' to a more general 'www' since we plan to use Nginx for other purposes as well. Now the Get data - Upload file does not work any longer because of file permissions. Files are uploaded correctly to a directory /local/data/galaxy_tmp/upload_**store/ but then are owned by the 'www' user and read-writeable by this other only. Thus, the Galaxy user 'galaxy' cannot open them, cannot determine the file type and the whole Upload file process fails. How can I set the file permissions of uploaded files? Do I need to enter a matching 'umask' in some Galaxy configuration or in some Nginx configuration file. Any links to where to set such a umask would be greatly appreciated. Thanks, Joern -- Joern Toedling, PhD Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de Tel.: +49 6131 39 21511 __**_ 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/
[galaxy-dev] upload multiple files
I noticed that when uploading multiple files only one job gets submitted to the queue. Is there a way for galaxy to split that up on multiple nodes? Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: icho...@illumina.commailto:icho...@illumina.com Website: www.illumina.comhttp://www.illumina.com ___ 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] tool which using web service
Shashi, You may find this wiki useful as well - sorry I missed it in my initial response. http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources On Aug 24, 2011, at 12:15 PM, Greg Von Kuster wrote: Hello Shashi, On Aug 24, 2011, at 11:55 AM, shashi shekhar wrote: i have an application ,from there i want input file in galaxy like usc_browser. in tools/data-source/ucsc_tablebrowser.xml u are passing some values from galaxy to ucsc_browser .and theen u are getting some info from ucsc browser. Yes i want to crate tool like this. can i get any documents for such type of tool. Take a look at the request_param_translation tag explanation in our tool config syntax wiki at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Crequest_param_translation.3E_tag_set thanks for reply On Wed, Aug 24, 2011 at 6:57 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Sashi, Look at our tool wikis at http://wiki.g2.bx.psu.edu/Admin/Tools You probably want to base your tool config file on ~/tools/data-source/ucsc_tablebrowser.xml. Greg Von kuster On Aug 24, 2011, at 9:12 AM, shashi shekhar wrote: hi, I have application , i want to integrate that application like ucsc_browser in my local instance of galaxy .Application create some input data ,that data i want to send into galaxy to process. can u help me how can i add such type of tool in Galaxy ? Regards shashi ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu Greg Von Kuster Galaxy Development Team g...@bx.psu.edu Greg Von Kuster Galaxy Development Team g...@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] Sam2interval.py bug
The read_name has been implemented as well. Thanks, K On Wed, Aug 24, 2011 at 1:15 PM, Kanwei Li kan...@gmail.com wrote: Hi Shaun, Thanks for reporting this, I have just committed the fix. I will let you know if we add the read_name to the truncated output. -K On Tue, Aug 2, 2011 at 6:54 AM, SHAUN WEBB swe...@staffmail.ed.ac.ukwrote: Hi, I've noticed a bug in sam2interval.py. There are a few indentation errors in the final lines of code. I think there should be an indent after: if not ref_name == '*': And this whole if statement should be included in the for loop above. Also, would you be able to add read_name to the truncated output (when not printing all fields). This makes downstream analysis a lot easier, e.g. looking at reads that map multiple times. Thanks Shaun Webb -- 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/ ___ 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] Galaxy public instances: data and job quotas
also, delete and purge a quota seems to have no effect. On Wed, Aug 24, 2011 at 3:58 PM, Edward Kirton eskir...@lbl.gov wrote: i created some quotas which were assigned to groups (set as for yes, registered users) but apparently the groups didn't initially stick; i had to edit the quota after creation to reassign the group. On Fri, Aug 19, 2011 at 4:44 PM, Jennifer Jackson j...@bx.psu.edu wrote: Galaxy public instances: data and job quotas User data and job quota limits are now implemented at the public Galaxy Test instance http://test.g2.bx.psu.edu: http://galaxyproject.org/Test#**Quotashttp://galaxyproject.org/Test#Quotas While no quotas are currently implemented at the public Galaxy Main instance http://usegalaxy.org, we do ask that users stay within certain usage limits: http://galaxyproject.org/Main#**Quotashttp://galaxyproject.org/Main#Quotas If you find that you require additional resources, please consider the alternative Galaxy options explained at: http://galaxyproject.org/Big%**20Picture/Choiceshttp://galaxyproject.org/Big%20Picture/Choices Thanks for using Galaxy! __**_ 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] Setting the output label based on input parameters?
Hi all, Is there a way to set the label of the output based on the input parameters? Perhaps by using the action tag? Basically, I want the output label to be different if the user sets a particular parameter to be true. - Nik. ___ 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] macs in galaxy
Yes. Thank you for your help :) -Original Message- From: Kanwei Li [mailto:kan...@gmail.com] Sent: Wednesday, August 24, 2011 11:28 PM To: KOH Jia Yu Jayce Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] macs in galaxy Hi Jayce, Are you running this on your local instance? It seems you are running MACS 1.4, which our wrapper does not support yet, but we are planning to add a wrapper for 1.4 soon. Thanks, K On Wed, Aug 24, 2011 at 4:20 AM, KOH Jia Yu Jayce ko...@gis.a-star.edu.sgmailto:ko...@gis.a-star.edu.sg wrote: In running macs in galaxy, the following error was found ERROR:root:mfold format error! Your input is '32'. It should be like '10,30' A format for mfold like 10,30 is expected... but the default value configured in xml remains as 32. will there be an updated version of this xml in future? Also after altering the default display mfold value to 10,30, type integer in the param tag for mfold become erroneous. May I ask what is the correct type for input format 10,30? Thanks alot ___ 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] Setting the output label based on input parameters?
Hi Nikhil, The tool templates are Cheetah templates, so you can do things like: outputs %if param == True: data format=txt name=blah label=Label1 / %else data format=txt name=blah label=Label2 / %endif /outputs Thanks, K On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi najo...@ucdavis.edu wrote: Hi all, Is there a way to set the label of the output based on the input parameters? Perhaps by using the action tag? Basically, I want the output label to be different if the user sets a particular parameter to be true. - Nik. ___ 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/
