[galaxy-dev] http://toolshed.g2.bx.psu.edu/ 502 Bad Gateway
Hi, Could someone take a look at the Tool Shed server please? I'm getting this for http://toolshed.g2.bx.psu.edu/ 502 Bad Gateway nginx/1.1.4 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] http://toolshed.g2.bx.psu.edu/ 502 Bad Gateway
Hi Peter, The tool shed should be functional now. Thanks for reporting this! Greg On May 25, 2012, at 6:08 AM, Peter Cock wrote: Hi, Could someone take a look at the Tool Shed server please? I'm getting this for http://toolshed.g2.bx.psu.edu/ 502 Bad Gateway nginx/1.1.4 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/ ___ 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] http://toolshed.g2.bx.psu.edu/ 502 Bad Gateway
Working fine as of now. --hk -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Peter Cock Sent: Friday, May 25, 2012 6:09 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] http://toolshed.g2.bx.psu.edu/ 502 Bad Gateway Hi, Could someone take a look at the Tool Shed server please? I'm getting this for http://toolshed.g2.bx.psu.edu/ 502 Bad Gateway nginx/1.1.4 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/ ___ 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] possible to resume failed workflow?
Jason, Are the affected workflow steps actually failing or are they falsely being reported as “failed” (have you checked if correct output exists for the affected step)? Once a step/job is marked “failed’ you can’t use the output (even if it exists) for any subsequent step. If you are using a cluster for your local galaxy install and NFS disk mounts then this may happen because of write cache delays. If that is the case, increasing the value for the “retry_job_output_collection” parameter to a higher number in the universe_wsgi.ini should help you get around the problem. It fixed the problem in our local galaxy where some jobs were being reported as “failed” though the correct output was there. --Hemant From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of J. Greenbaum Sent: Thursday, May 24, 2012 9:18 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] possible to resume failed workflow? Hi, I've created a few workflows and have been having issues with some steps randomly failing. This would not be an issue if I could simply resume the workflow from the failed step, but it seems that this is not possible. Instead, I'm forced to restart the workflow from the beginning. Is this true or am I missing something? Thanks, Jason -- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgb...@liai.orgmailto:jgb...@liai.org La Jolla Institute for Allergy and Immunology ___ 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] How must I configure Apache ?
Yes a follow this wiki but it doesn't work. I've tried to post too in
apache forum because may be it's simply a problem with apache.
thank you for your help.
Julie
2012/5/24 Carlos Borroto carlos.borr...@gmail.com
Glad it helped.
About configuring Galaxy to use port 8080, other than what you are
already doing, checking for another process already using the port, I
wouldn't know what to recommend.
About the balancing configuration, I haven't done it, so I don't have
much to help with that. I do think it should go in the virtual host
configuration file(default) and I don't think it should matter if you
put it before or after the rewrite rules.
Are you following the instructions in?:
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling
Regards,
Carlos
On Mon, May 21, 2012 at 4:17 AM, julie dubois dubju...@gmail.com wrote:
Hi,
Thanks for your answer.
Effectively it's not necessary on integrating Galaxy with a third party
authentication system.
I've integrated my configuration to the file default and it's work !
Just one remark. I've configured the file ports.conf with the line :
Listen 8080, and it didn't work!
In fact, the shell says me that the galaxy port was already in use while
the
command lsof -ti : 8080 showed no result.
And when I delete the line listen 8080 of my file ports.conf, Galaxy
work!
Is it normal ?
Finally, if I want tu use the proxy balancer lines like this (it is in
the
hope to increase performances):
Proxy balancer://galaxy
Balancer member...
...
/Proxy
must I add in default file (and before or after the rewrite rules?) or
in an
other file ?
Thank you in advance.
Julie
2012/5/18 Carlos Borroto carlos.borr...@gmail.com
Hi Julie,
Could you answer a couple of questions?
First, are you interested on integrating Galaxy with a third party
authentication system?
Second, do you expect heavy usage(I would say hundreds of concurrent
users) where you would need several Galaxy servers with the work load
balanced amount them?. Note even if you only have one Galaxy server,
you will still have several Apache processes running and you will be
able to serve multiple concurrent users without issue. Well at least
from the web server side of things, if you expect even a moderate
usage you should use a database back-end like PostgreSQL or MySQL.
If the answer to these questions is no, all you need in a
Debian/Ubuntu system is to place this in
'/etc/apache2/sites-available/default' file between the VirtualHost
tags:
RewriteEngine on
RewriteRule ^/static/style/(.*)
/home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/scripts/(.*)
/home/nate/galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule ^/static/(.*) /home/nate/galaxy-dist/static/$1 [L]
RewriteRule ^/favicon.ico /home/nate/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/robots.txt /home/nate/galaxy-dist/static/robots.txt [L]
RewriteRule ^(.*) http://localhost:8080$1 [P]
Even if the answer if yes to both questions, I would start with the
simpler setup first, get it working and then grow from there.
Hope it helps,
Carlos
On Fri, May 18, 2012 at 6:59 AM, julie dubois dubju...@gmail.com
wrote:
Hi,
First, Sorry but, I'm a newbie with Apache and my questions will
certainly
appear stupid.
To configure apache2, I've followed this wiki :
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
And I write these instructions :
Proxy http://localhost:8080
Order deny,allow
Allow from all
/Proxy
RewriteEngine on
Location /
# Define the authentication method
AuthType Basic
AuthName Galaxy
AuthUserFile /home/nate/htpasswd
Require valid-user
# Take the $REMOTE_USER environment variable and set it as a
header
in
the proxy request.
RewriteCond %{IS_SUBREQ} ^false$
RewriteCond %{LA-U:REMOTE_USER} (.+)
RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER %{RU}e
/Location
RewriteRule ^/static/style/(.*)
/home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/(.*) /home/nate/galaxy-dist/static/$1 [L]
RewriteRule ^/favicon.ico /home/nate/galaxy-dist/static/favicon.ico
[L]
RewriteRule ^/robots.txt /home/nate/galaxy-dist/static/robots.txt [L]
RewriteRule ^(.*) http://localhost:8080$1 [P]
/Location
But several problems appeared when I launched my Galaxy.
First, must this instructions block be in the file apache2.conf or in
the
file default of sites-available directory ?
If it must be in the file default, is it between the VirtualHost
tags
or
out of these tags ?
Second, I've created an htpaswd file in my home directory, but when I
launch
galaxy, it doesn't request me a login and password but it says me that
Galaxy requires an user
Re: [galaxy-dev] Batch limit on Wokflows
Is it possible to use multiple 'input dataset' steps in a single workflow in batch? If I have two, I can only select batch input on one of them. If one is open, the other toggle button does not respond. Thanks, Geert On 02/14/2012 09:55 PM, Petit III, Robert A. wrote: Thats it! Consider this resolved, and total operator error. I tried using the 'Input Dataset' step, and am no longer having issues. Thanks for the help Dannon. From: Petit III, Robert A. Sent: Tuesday, February 14, 2012 3:49 PM To: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Batch limit on Wokflows Workflow is beginning directly with a tool. An example test workflow I've been trying is, I have 20 fasta files, and the workflow has only the FASTA-to-Tabular tool. Thanks, Robert From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, February 14, 2012 3:33 PM To: Petit III, Robert A. Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Batch limit on Wokflows I hadn't had a chance to follow up again yet, but in your workflow, are you using an Input Dataset step, or do you have the workflow beginning directly with a tool? -Dannon On Feb 14, 2012, at 3:26 PM, Petit III, Robert A. wrote: Here's the latest. I have tested this on Chrome, Firefox, and IE. I've tried the latest revisions of galaxy-central (71031bf3105c) and galaxy-dist (26920e20157f) straight out of the box (hg clone, sh run.sh, go to localhost:8080). I am still running into same issue. All is well with 19 or less datasets in the history, but as soon as I add a 20th I can no longer run a workflow on multiple datasets. Are there any known issues running galaxy on Ubuntu 10.04? This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ 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/ -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 ___ 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] http://toolshed.g2.bx.psu.edu/ 502 Bad Gateway
On Fri, May 25, 2012 at 12:03 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, The tool shed should be functional now. Thanks for reporting this! Greg It was working again when I got your email, but while I was out to lunch it has gone back to Error 502 Bad Gateway :( 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] Batch limit on Wokflows
I'm looking for a workflow of : Forward reads.fastq = QC = map = etc Reverse reads.fastq = and would like to specify pairs of files (from MiSeq) in the batch workflow interface. I'm currently looking into interlacing the files outside of galaxy before uploading. Then I can de-interlace as the first step, but this is redundant, as we get seperate files to start. Best regards, Geert On 05/25/2012 02:12 PM, Dannon Baker wrote: Batch mode is currently only allowed for a single input dataset step, so the others are intentionally disabled upon toggling the first one on. We do, however, plan to eventually expand this to allow for pairwise/etc input sets. Out of curiosity, which behavior is it that you're looking for? -Dannon On May 25, 2012, at 8:03 AM, Geert Vandeweyer wrote: Is it possible to use multiple 'input dataset' steps in a single workflow in batch? If I have two, I can only select batch input on one of them. If one is open, the other toggle button does not respond. Thanks, Geert On 02/14/2012 09:55 PM, Petit III, Robert A. wrote: Thats it! Consider this resolved, and total operator error. I tried using the 'Input Dataset' step, and am no longer having issues. Thanks for the help Dannon. From: Petit III, Robert A. Sent: Tuesday, February 14, 2012 3:49 PM To: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] Batch limit on Wokflows Workflow is beginning directly with a tool. An example test workflow I've been trying is, I have 20 fasta files, and the workflow has only the FASTA-to-Tabular tool. Thanks, Robert From: Dannon Baker [dannonba...@me.com] Sent: Tuesday, February 14, 2012 3:33 PM To: Petit III, Robert A. Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Batch limit on Wokflows I hadn't had a chance to follow up again yet, but in your workflow, are you using an Input Dataset step, or do you have the workflow beginning directly with a tool? -Dannon On Feb 14, 2012, at 3:26 PM, Petit III, Robert A. wrote: Here's the latest. I have tested this on Chrome, Firefox, and IE. I've tried the latest revisions of galaxy-central (71031bf3105c) and galaxy-dist (26920e20157f) straight out of the box (hg clone, sh run.sh, go to localhost:8080). I am still running into same issue. All is well with 19 or less datasets in the history, but as soon as I add a 20th I can no longer run a workflow on multiple datasets. Are there any known issues running galaxy on Ubuntu 10.04? This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ 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/ -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 ___ 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/ -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 ___ 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] Avoid to download output files
It works !!! I've changed the extension of output file of an application. But in Galaxy, it's referenced over the old file with .dat in history, so if we want to re-use this file with other tool it's not the best way to change this extension after the run of tool. If I could change the extension before the chargement in history, that would be perfect. But I suppose it's not possible. I'm already satisfied of the possibility I've discover with the modification of xml files. Thank you for your help Julie 2012/5/24 Peter Cock p.j.a.c...@googlemail.com On Thu, May 24, 2012 at 3:27 PM, julie dubois dubju...@gmail.com wrote: Ok I've tried to add my script perl in the command line with semi-colon. It's work But this script sets in entry the variable $wigoutput of my file xml. But when I show it, it's not what I want; It's just the value : 1 . I think it's because the script of the application (macs) is called before my script, the $wigoutput doesn't contain the good value when it stops. It is what I think, it's not possible to change the extension. Thank you for your attention and your answers Julie Well, yes, if you do this at the command line: cmdA; cmdB then cmdA is executed before cmdB. Try it yourself at the Unix/Linux prompt, e.g. date; ls compared to: ls; date If you want to run it first, try putting your script BEFORE the existing entry in the tool XML's command tag. 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] possible to resume failed workflow?
Jason, Is there a possibility that the jobs failing to submit because there is no valid input detected (because of a write cache delay perhaps)? Sorry I do not know PBS. We use LSF and we have ended up increasing the “retry_job_output_collection” entry to 30 to catch these falsely “failed” jobs. --Hemant From: J. Greenbaum [mailto:jgb...@liai.org] Sent: Friday, May 25, 2012 11:42 AM To: Kelkar, Hemant Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] possible to resume failed workflow? Hi Hermant, Thanks for the suggestion. I've tried setting that parameter to 5, but it has not helped. I've noticed in the galaxy server output that I'm getting the following error: galaxy.jobs.runners.pbs DEBUG 2012-05-25 08:13:17,957 (96) pbs_submit failed, PBS error 15031: Protocol (ASN.1) error I believe this is why certain jobs are failing. I've googled a bit for this error, and found many threads where similar problems were reported. Here are a couple: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-February/004336.html http://osdir.com/ml/galaxy-development-source-control/2011-02/msg00148.html Is anyone aware of a solution to this issue? Thanks, J -- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgb...@liai.orgmailto:jgb...@liai.org La Jolla Institute for Allergy and Immunology From: Hemant Kelkar hkel...@unc.edumailto:hkel...@unc.edu To: J. Greenbaum jgb...@liai.orgmailto:jgb...@liai.org, galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Sent: Friday, May 25, 2012 4:34:12 AM Subject: RE: [galaxy-dev] possible to resume failed workflow? Jason, Are the affected workflow steps actually failing or are they falsely being reported as “failed” (have you checked if correct output exists for the affected step)? Once a step/job is marked “failed’ you can’t use the output (even if it exists) for any subsequent step. If you are using a cluster for your local galaxy install and NFS disk mounts then this may happen because of write cache delays. If that is the case, increasing the value for the “retry_job_output_collection” parameter to a higher number in the universe_wsgi.ini should help you get around the problem. It fixed the problem in our local galaxy where some jobs were being reported as “failed” though the correct output was there. --Hemant From: galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu]mailto:[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of J. Greenbaum Sent: Thursday, May 24, 2012 9:18 PM To: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] possible to resume failed workflow? Hi, I've created a few workflows and have been having issues with some steps randomly failing. This would not be an issue if I could simply resume the workflow from the failed step, but it seems that this is not possible. Instead, I'm forced to restart the workflow from the beginning. Is this true or am I missing something? Thanks, Jason -- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgb...@liai.orgmailto:jgb...@liai.org La Jolla Institute for Allergy and Immunology ___ 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] HMMER wrappers
On Fri, May 25, 2012 at 4:54 PM, Peter Cock p.j.a.c...@googlemail.comwrote: I ran into some similar problems wrapping other tools giving table based output, and used a wrapper script to make them into tab separated tables for use in Galaxy. e.g. SignalP 3 (spaces), EffectiveT4 (semi-colons). Sorry, that was a typo for EffectiveT3 from http://effectors.org/ (my wrapper is on the Tool Shed). 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/
[galaxy-dev] Proftpd Problem
Hi, I'am trying to set up ProFTP on Debain to enable FTP upload on Galaxy installed locally? I followed the instructions on this link ( http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP) but it doesn't work. When I restart proftpd i get this message : mod_tls_memcache/0.1: notice: unable to register 'memcache' SSL session cache: Memcache support not enabled Thanks, Amine ___ 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/
