Re: [galaxy-user] History not updating for multiple instances of Galaxy
Further, when I try "register" I add an email address and password, but the system still doesn't log me in Maybe this is a database configuration issue? I didn't think I'd need to state any specific entries in universe as I am using physically separate directories i.e. /home/galaxy/galaxy-cte/ i.e. /home/galaxy/galaxy-Newcastle/ Cheers Neil From: Burdett, Neil (ICT Centre, Herston - RBWH) Sent: Thursday, 21 February 2013 1:19 PM To: galaxy-...@lists.bx.psu.edu Cc: galaxy-user@lists.bx.psu.edu Subject: History not updating for multiple instances of Galaxy Hi, I have three instances of galaxy running on the same Linux box. My "/etc/apache2/sites-available/default" is: RewriteEngine on RewriteRule ^/galaxy-csiro$ /galaxy-csiro/ [R] RewriteRule ^/galaxy-csiro/static/style/(.*) /home/galaxy/galaxy-csiro/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-csiro/static/scripts/(.*) /home/galaxy/galaxy-csiro/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-csiro/static/(.*) /home/galaxy/galaxy-csiro/static/$1 [L] RewriteRule ^/galaxy-csiro/favicon.ico /home/galaxy/galaxy-csiro/static/favicon.ico [L] RewriteRule ^/galaxy-csiro/robots.txt /home/galaxy/galaxy-csiro/static/robots.txt [L] RewriteRule ^/galaxy-csiro(.*) http://localhost:9080$1 [P] RewriteRule ^/galaxy-cte$ /galaxy-cte/ [R] RewriteRule ^/galaxy-cte/static/style/(.*) /home/galaxy/galaxy-cte/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-cte/static/scripts/(.*) /home/galaxy/galaxy-cte/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-cte/static/(.*) /home/galaxy/galaxy-cte/static/$1 [L] RewriteRule ^/galaxy-cte/favicon.ico /home/galaxy/galaxy-cte/static/favicon.ico [L] RewriteRule ^/galaxy-cte/robots.txt /home/galaxy/galaxy-cte/static/robots.txt [L] RewriteRule ^/galaxy-cte(.*) http://localhost:9000$1 [P] RewriteRule ^/galaxy-Newcastle$ /galaxy-Newcastle/ [R] RewriteRule ^/galaxy-Newcastle/static/style/(.*) /home/galaxy/galaxy-Newcastle/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-Newcastle/static/scripts/(.*) /home/galaxy/galaxy-Newcastle/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-Newcastle/static/(.*) /home/galaxy/galaxy-Newcastle/static/$1 [L] RewriteRule ^/galaxy-Newcastle/favicon.ico /home/galaxy/galaxy-Newcastle/static/favicon.ico [L] RewriteRule ^/galaxy-Newcastle/robots.txt /home/galaxy/galaxy-Newcastle/static/robots.txt [L] RewriteRule ^/galaxy-Newcastle(.*) http://localhost:9010$1 [P] I can view all the instances However, when I try and "Get Data" and upload a file the history side panel remains empty. I can see that the files have been uploaded to (for example) % ls -lrt galaxy-Newcastle/database/files/000/ total 22868 -rw-rw-r-- 1 galaxy galaxy 23017819 Feb 21 13:01 dataset_1.dat -rw-rw-r-- 1 galaxy galaxy 187339 Feb 21 13:02 dataset_2.dat -rw-rw-r-- 1 galaxy galaxy 206568 Feb 21 13:03 dataset_3.dat Any ideas much appreciated... The log file state: Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342321 127.0.0.1 - - [21/Feb/2013:13:16:21 +1000] "GET /galaxy-Newcastle/tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/root/tool_menu"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" galaxy.web.framework DEBUG 2013-02-21 13:16:28,630 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,630 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "POST /galaxy-Newcastle/tool_runner/upload_async_create HTTP/1.1" 500 - "http://barium-rbh/galaxy-Newcastle/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342322 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "GET
[galaxy-user] History not updating for multiple instances of Galaxy
Hi, I have three instances of galaxy running on the same Linux box. My "/etc/apache2/sites-available/default" is: RewriteEngine on RewriteRule ^/galaxy-csiro$ /galaxy-csiro/ [R] RewriteRule ^/galaxy-csiro/static/style/(.*) /home/galaxy/galaxy-csiro/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-csiro/static/scripts/(.*) /home/galaxy/galaxy-csiro/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-csiro/static/(.*) /home/galaxy/galaxy-csiro/static/$1 [L] RewriteRule ^/galaxy-csiro/favicon.ico /home/galaxy/galaxy-csiro/static/favicon.ico [L] RewriteRule ^/galaxy-csiro/robots.txt /home/galaxy/galaxy-csiro/static/robots.txt [L] RewriteRule ^/galaxy-csiro(.*) http://localhost:9080$1 [P] RewriteRule ^/galaxy-cte$ /galaxy-cte/ [R] RewriteRule ^/galaxy-cte/static/style/(.*) /home/galaxy/galaxy-cte/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-cte/static/scripts/(.*) /home/galaxy/galaxy-cte/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-cte/static/(.*) /home/galaxy/galaxy-cte/static/$1 [L] RewriteRule ^/galaxy-cte/favicon.ico /home/galaxy/galaxy-cte/static/favicon.ico [L] RewriteRule ^/galaxy-cte/robots.txt /home/galaxy/galaxy-cte/static/robots.txt [L] RewriteRule ^/galaxy-cte(.*) http://localhost:9000$1 [P] RewriteRule ^/galaxy-Newcastle$ /galaxy-Newcastle/ [R] RewriteRule ^/galaxy-Newcastle/static/style/(.*) /home/galaxy/galaxy-Newcastle/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-Newcastle/static/scripts/(.*) /home/galaxy/galaxy-Newcastle/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-Newcastle/static/(.*) /home/galaxy/galaxy-Newcastle/static/$1 [L] RewriteRule ^/galaxy-Newcastle/favicon.ico /home/galaxy/galaxy-Newcastle/static/favicon.ico [L] RewriteRule ^/galaxy-Newcastle/robots.txt /home/galaxy/galaxy-Newcastle/static/robots.txt [L] RewriteRule ^/galaxy-Newcastle(.*) http://localhost:9010$1 [P] I can view all the instances However, when I try and "Get Data" and upload a file the history side panel remains empty. I can see that the files have been uploaded to (for example) % ls -lrt galaxy-Newcastle/database/files/000/ total 22868 -rw-rw-r-- 1 galaxy galaxy 23017819 Feb 21 13:01 dataset_1.dat -rw-rw-r-- 1 galaxy galaxy 187339 Feb 21 13:02 dataset_2.dat -rw-rw-r-- 1 galaxy galaxy 206568 Feb 21 13:03 dataset_3.dat Any ideas much appreciated... The log file state: Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342321 127.0.0.1 - - [21/Feb/2013:13:16:21 +1000] "GET /galaxy-Newcastle/tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/root/tool_menu"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" galaxy.web.framework DEBUG 2013-02-21 13:16:28,630 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,630 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "POST /galaxy-Newcastle/tool_runner/upload_async_create HTTP/1.1" 500 - "http://barium-rbh/galaxy-Newcastle/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342322 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "GET /galaxy-Newcastle/tool_runner/upload_async_message HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "GET /galaxy-Newcastle/history HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_message"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" galaxy.web.framework DEBUG 2013-02-21 13:16:29,261 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/root/user
Re: [galaxy-user] Problem Loading History Pane
Hello Lizex,
The utility tools from Tophat are not included with Galaxy, so that is
perhaps why you are having trouble creating junctions files, but I am
wondering if you need them at all.
You mention that you have different sequence types from different
samples. These represent different conditions? Or some do and others are
replicates or complete replacements for the originals (the re-sequenced
data)?
For data representing different samples/conditions, you would not want
to map the data together with Tophat or run it together in Cufflinks.
Even replicates are not mapped in the same Tophat job, although they are
included in the same Cufflinks job. The tool authors have an opinion
about the value of replicates - so be sure to read about that at the
Cufflinks web site.
http://cufflinks.cbcb.umd.edu/howitworks.html#reps
The first time different conditions would be in the same job would be at
the stage where Cuffmerge is run, to prepare for Cuffdiff - where the
differential expression analysis would take place. This is past the
stage where individual reads are involved.
Our RNA-seq tutorial is here:
https://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
And several donated by the Galaxy community are here:
http://wiki.galaxyproject.org/Learn#Other_Tutorials
But the best resource is the paper from the tool authors ("Protocol"):
http://tophat.cbcb.umd.edu/manual.html
http://cufflinks.cbcb.umd.edu/manual.html
In the end, you may decide that some of the complexity of your data can
be reduced by dropping some datasets, to simplify and achieve the same
overall results, or perhaps even improved results. In general, I think
it is probably safe to say that the less "done" to prep expression data,
and certainly the more homogeneous it is, the better the result. But
this is your decision.
Good luck with your project. Next time when asking a question, please
open a brand new email message and start a new thread, not reply to an
existing thread and just change the subject line. This helps us with
tracking and is appreciated.
Thanks!
Jen
Galaxy team
On 2/16/13 5:23 AM, Lizex Husselmann wrote:
Dear all
I have in my project single end reads (50 bp) for some samples and
paired end reads (100 bp frw and rev) for the other samples. I had to
re-sequence some of the samples of which I have paired-end reads.
However the re-sequence data I receives is single-end reads of 250 bp.
Tophat wont allow mapping single and paired-end reads together. It says
the result will look bad. They do mention that you can convert the
junctions.bed file (output of Tophat) with bed_to_juncs using the -j
option. I quote for TopHat manual "run TopHat on the 2nd set of reads
using the -j option to supply the junctions file produced by be_to_juncs
in the previous step". This is supposed to work but I didn't get it to
work. Any suggestion on how I should go about analyzing this data?
Kind regards
Lizex
>>> Nate Coraor 02/15/13 5:48 PM >>>
On Feb 15, 2013, at 10:35 AM, Mike Dufault wrote:
> To whom it may concern:
>
> The History panel on the right side of the Galaxy page is taking a
very very long time to load. Also, when it does load, I have tired to
save my .bam files and the transmissions gets truncated to ~7000kb -
8000kb of data. All of my .bam files are several GB.
>
> Some times, when I retry tor download the data, it succeeds and other
times it is again truncated. The size of the truncation may be different
for the same file on the retry attempt.
>
> Is there a problem with Galaxy?
Hi Mike,
There are some performance problems with the Main site that we are
currently investigating Thanks for the information and we apologize for
the problems.
--nate
>
> Thanks,
> Mike
> ___
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[galaxy-user] Post Galaxy-ChIP-seq analysis: UCSC Genome browser can't read the wig file
Thank you very much Jennifer! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Post Galaxy-ChIP-seq analysis: UCSC Genome browser can't read the wig file
Hello Bodour, If the genome you are using as at UCSC, then yes, the BED and Interval files will have a link to UCSC, but the wig files will not by default. To view the wig data, you can use the Galaxy Track browser or IGB directly, or convert the file to bigWig and then view it at UCSC with the tool "Convert Formats -> Wig/BedGraph-to-bigWig". The "PEAKS" bed file is the primary output of the tool. The other data files are supporting evidence or alternate views. Bringing up all the data together in a browser would be a good way to understand how they fit together. View the original MACS documentation: http://liulab.dfci.harvard.edu/MACS/00README.html And tutorials including MACS are here: - https://main.g2.bx.psu.edu/u/james/p/exercise-chip-seq - https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 (protocol 3) - http://wiki.galaxyproject.org/Learn#Other_Tutorials -> Analysis of ChIP-seq data in Galaxy Hopefully this helps, Jen Galaxy team On 2/20/13 8:33 AM, Bodour Al-Khamees wrote: Hello, I am using the Galaxy web tool to analyze ChIP-seq data. By applying MACS algorithm, the Galaxy browser generated bed and wig files. Within the Galaxy browser, the bed file has a link to the UCSC Genome browser whereas the wig file has no link to the UCSC browser. I wonder which file is best to visualize the peaks in the UCSC Genome browser and how? Any experience or just thoughts? Thank you very much in advance! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Welcome to the "galaxy-user" mailing list (Digest mode)
Of course! Any subscriber can post -- it looks like your message "Post Galaxy-ChIP-seq analysis: UCSC Genome browser can't read the wig file" went through correctly. Thanks for your interest. -Dannon On Wed, Feb 20, 2013 at 11:36 AM, Bodour Al-Khamees wrote: > Hello, > > I would like to ask few question. I wonder if I can post in this mailing > list. > > > Thank you very much! > Bodour > > > On Wed, Feb 20, 2013 at 11:28 AM, > wrote: >> >> Welcome to the galaxy-user@lists.bx.psu.edu mailing list! The Galaxy >> User list is for the discussion of analysis techniques in Galaxy and >> use of other features on the public Galaxy server at usegalaxy.org. >> For discussion of all topics pertaining to local Galaxy installations >> including tool integration, server configuration, and modifications to >> the Galaxy source code, please subscribe to the Galaxy Development >> list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To post to this list, send your email to: >> >> galaxy-user@lists.bx.psu.edu >> >> General information about the mailing list is at: >> >> http://lists.bx.psu.edu/listinfo/galaxy-user >> >> If you ever want to unsubscribe or change your options (eg, switch to >> or from digest mode, change your password, etc.), visit your >> subscription page at: >> >> http://lists.bx.psu.edu/options/galaxy-user/alkhameesbodour%40gmail.com >> >> >> You can also make such adjustments via email by sending a message to: >> >> galaxy-user-requ...@lists.bx.psu.edu >> >> with the word `help' in the subject or body (don't include the >> quotes), and you will get back a message with instructions. >> >> You must know your password to change your options (including changing >> the password, itself) or to unsubscribe. It is: >> >> 1234 >> >> Normally, Mailman will remind you of your lists.bx.psu.edu mailing >> list passwords once every month, although you can disable this if you >> prefer. This reminder will also include instructions on how to >> unsubscribe or change your account options. There is also a button on >> your options page that will email your current password to you. > > > > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Welcome to the "galaxy-user" mailing list (Digest mode)
Hello, I would like to ask few question. I wonder if I can post in this mailing list. Thank you very much! Bodour On Wed, Feb 20, 2013 at 11:28 AM, wrote: > Welcome to the galaxy-user@lists.bx.psu.edu mailing list! The Galaxy > User list is for the discussion of analysis techniques in Galaxy and > use of other features on the public Galaxy server at usegalaxy.org. > For discussion of all topics pertaining to local Galaxy installations > including tool integration, server configuration, and modifications to > the Galaxy source code, please subscribe to the Galaxy Development > list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To post to this list, send your email to: > > galaxy-user@lists.bx.psu.edu > > General information about the mailing list is at: > > http://lists.bx.psu.edu/listinfo/galaxy-user > > If you ever want to unsubscribe or change your options (eg, switch to > or from digest mode, change your password, etc.), visit your > subscription page at: > > http://lists.bx.psu.edu/options/galaxy-user/alkhameesbodour%40gmail.com > > > You can also make such adjustments via email by sending a message to: > > galaxy-user-requ...@lists.bx.psu.edu > > with the word `help' in the subject or body (don't include the > quotes), and you will get back a message with instructions. > > You must know your password to change your options (including changing > the password, itself) or to unsubscribe. It is: > > 1234 > > Normally, Mailman will remind you of your lists.bx.psu.edu mailing > list passwords once every month, although you can disable this if you > prefer. This reminder will also include instructions on how to > unsubscribe or change your account options. There is also a button on > your options page that will email your current password to you. > ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Post Galaxy-ChIP-seq analysis: UCSC Genome browser can't read the wig file
Hello, I am using the Galaxy web tool to analyze ChIP-seq data. By applying MACS algorithm, the Galaxy browser generated bed and wig files. Within the Galaxy browser, the bed file has a link to the UCSC Genome browser whereas the wig file has no link to the UCSC browser. I wonder which file is best to visualize the peaks in the UCSC Genome browser and how? Any experience or just thoughts? Thank you very much in advance! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
