Re: [galaxy-dev] Intersect multiple sorted BED files / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened

2014-04-25 Thread Sarah Maman
! /Update now! /** ** Here's how - https://wiki.galaxyproject.org/Support/Biostar** * On 4/22/14 3:25 AM, Sarah Maman wrote: Hello, I try to use Intersect multiple sorted BED files tool without success. A genome_test have been added in galaxy (genome_test.len in galaxy-dist/tool-data/shared/ucsc

[galaxy-dev] Add a private genome in database/build , only visible for a specific user connected on a local instance.

2014-04-14 Thread Sarah Maman
for others users. Should I specify something in galaxy-dist/tool-data/shared/ucsc/builds.txt file ? Thanks in advance, Sarah Maman -- --*-- Sarah Maman INRA - GenPhySE - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel

[galaxy-dev] Error at initialization of module heapycTraceback / Last sources of Galaxy

2013-08-12 Thread Sarah Maman
setsc import BitSet# base bitset type ImportError: /usr/local/bioinfo/src/galaxy-dev/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/sets/setsc.so: undefined symbol: _PyLong_AsScaledDouble Coul you please help me ? Thanks in advance, Sarah -- --*-- Sarah Maman INRA

[galaxy-dev] IVG display error / local instance of Galaxy

2013-06-10 Thread Sarah Maman
/to/my/galaxy/database/files/$1 [L] | | Do you have any idea ? Could you please help me ? Thanks in advance, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0

[galaxy-dev] Error / import rpy module

2013-06-05 Thread Sarah Maman
the eggs ' import does not allow the use of rpy module? How to debug these tools? Thnaks in advance, Sarah -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax

Re: [galaxy-dev] Error / import rpy module

2013-06-05 Thread Sarah Maman
3.0 Although we haven't started to us it, I recommend using rpy2: http://rpy.sourceforge.net/rpy2.html Most tools have been refactored by John Chilton see: http://dev.list.galaxyproject.org/rpy2-Core-Tools-td4659832.html Regards, Hans-Rudolf On 06/05/2013 10:19 AM, Sarah Maman wrote: Hello

Re: [galaxy-dev] Run galaxy on a specific SGE queue

2013-06-03 Thread Sarah Maman
Thanks Nate, In fact, our ~/.sge_request set workq by default. So, we have changed this parameter in ~/.sge_request file in order to change the working queue. Thanks again for your help, Sarah Nate Coraor a écrit : On May 22, 2013, at 11:36 AM, Sarah Maman wrote: Hi everyone

[galaxy-dev] Information for Galaxy Event Horizon

2013-05-30 Thread Sarah Maman
Event Horizon? Sincerely, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53

[galaxy-dev] Run galaxy on a specific SGE queue

2013-05-22 Thread Sarah Maman
-- Sarah Maman INRA - LGC - SIGENAE Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 ___ Please keep all replies on the list by using reply all in your mail

[galaxy-dev] Set upload from EBI SRA tool in a local instance of Galaxy

2013-04-19 Thread Sarah Maman
? Thank you in advance, Sarah -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53

[galaxy-dev] Step 3 of get Microbial Data install

2013-04-19 Thread Sarah Maman
:47 . Could you please, hel me ? Thnaks in advance, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53

Re: [galaxy-dev] Tophat didn't run

2013-04-16 Thread Sarah Maman
. Thank you again for your help, Sarah Jennifer Jackson a écrit : Hi Sarah, On 4/11/13 8:02 AM, Sarah Maman wrote: Thnaks Jennifer, Excuse me, my previous mail contains an error : In fact, the reference genome from my history was a fasta format (the name was GTF file but the format was fasta

Re: [galaxy-dev] Tophat didn't run

2013-04-11 Thread Sarah Maman
team On 4/10/13 3:15 AM, Sarah Maman wrote: Hello, When I run tophat (Tophat for Illumina Find splice junctions using RNA-seq data ), the job failed with truncated files. However, index files are available and I get exactly the same error message using built-in index or one of my history

[galaxy-dev] Tophat didn't run

2013-04-10 Thread Sarah Maman
10 09:17:12 CEST 2013 / In this post (http://dev.list.galaxyproject.org/tophat-for-illumina-looking-in-wrong-directory-for-bowtie2-indexes-tt4658609.html#none), the solution isn't found. Do you have any idea, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http

[galaxy-dev] hg pull aborted

2012-12-13 Thread Sarah Maman
Hello, When updating local instance of our Galaxy, the hg aborted: pulling from https://bitbucket.org/galaxy/galaxy-dist/ searching for changes adding changesets adding manifests adding file changes added 1482 changesets with 3989 changes to 1340 files abort: untracked file in working directory

Re: [galaxy-dev] Server Error / Edit attribut of a dataset generated by a tool

2012-12-13 Thread Sarah Maman
try and let you know. Sarah Daniel Blankenberg d...@bx.psu.edu a écrit : Hi Sarah, This looks to be due to a non-unicode character in the dataset's info field. Are you using a Galaxy revision = 7563:fca4e12478d6? Thanks for using Galaxy, Dan On Dec 11, 2012, at 8:25 AM, Sarah Maman wrote

[galaxy-dev] Server Error / Edit attribut of a dataset generated by a tool

2012-12-11 Thread Sarah Maman
Hello, One of my users gets the following message when he wishes to edit the attribute of a dataset which is generated by using a tool (same problem as it is a tool provided by Galaxy or a tool coded by us). Do you have any idea? Thanks in advance, Sarah Maman URL: http://sigenae

[galaxy-dev] Impossible to add a (new) tool in a workflow (in edition mode)

2012-12-11 Thread Sarah Maman
Hello, For one of my tools that I have added to my local instance of Galaxy, I can not add this tool in the editing workflow. When I click on the tool name in the tools windows on the left, it does not appear in the editing workflow. Do you have any idea? Thank you in advance, Sarah Maman

Re: [galaxy-dev] Impossible to add a (new) tool in a workflow (in edition mode)

2012-12-11 Thread Sarah Maman
Others actions are listed by not my click on this tool's name. Is paster.log file a default file of Galaxy? Where could I find this file ? Sarah Dannon Baker a écrit : Do you see any errors in Galaxy's paster.log, or in the javascript console? -Dannon On Dec 11, 2012, at 8:40 AM, Sarah Maman

Re: [galaxy-dev] Impossible to add a (new) tool in a workflow (in edition mode)

2012-12-11 Thread Sarah Maman
. So, no obvious errors there. Could you check for javascript console errors? And, if you'd like, feel free to send the tool xml to me directly and I'll try to see if I can reproduce the issue. -Dannon On Dec 11, 2012, at 10:47 AM, Sarah Maman sarah.ma...@toulouse.inra.fr wrote: Thanks

[galaxy-dev] How to modify save icon

2012-12-10 Thread Sarah Maman
Hello, The tool SAM to BAM generates a dataset from which it is possible to download two files (instead of one) from the icon save. As my script generates an output result and another txt output containing information about linux command, I will wish not to generate two datasets in history

[galaxy-dev] GFF tools

2012-07-30 Thread Sarah Maman
object could be decoded: line 1 column 0 (char 0) Could you please help me ? Thanks in advance, Sarah Maman ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy

Re: [galaxy-dev] Tool added / pb with output file

2012-07-20 Thread Sarah Maman
script have been modified). Faithfully, Sarah Maman Sarah Maman a écrit : Hello, I have added a tool in my local instance to map BAM files on reference genome fasta file thanks to BWA. This tool runs, and the output file generated in database/files/000 is correct (not empty and good data

[galaxy-dev] Tool added / pb with output file

2012-07-16 Thread Sarah Maman
Hello, I have added a tool in my local instance to map BAM files on reference genome fasta file thanks to BWA. This tool runs, and the output file generated in database/files/000 is correct (not empty and good data inside) but the output listed in the history panel of Galaxy interface , is

[galaxy-dev] DrmCommunicationException: code 2: unable to contact qmaster using port 6444 on host login

2012-06-28 Thread Sarah Maman
-after-DrmCommunicationException-td3651225.html Could you please help me ? Thanks in advance, Sarah Maman ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy

Re: [galaxy-dev] MarkupSafe cannot be fetched

2012-05-09 Thread Sarah Maman
have been updated except for Markupsafe. So I downloaded Markupsafe from Python website. Since then I have no warning on my runs ;-) Thanks, Sarah Nate Coraor a écrit : On Apr 27, 2012, at 6:00 AM, Sarah Maman wrote: Hello, After pulling latest changes (March 2012 - r 40f1816d6857

Re: [galaxy-dev] MarkupSafe cannot be fetched

2012-05-04 Thread Sarah Maman
node. If I run `python ./scripts/fetch_eggs.py` in galaxy-dist directory, as Galaxy user, but on my virtual machine, missing eggs are not grabed. Do you have another solution? Thanks, Sarah Nate Coraor a écrit : On Apr 27, 2012, at 6:00 AM, Sarah Maman wrote: Hello, After pulling

Re: [galaxy-dev] Interested in speaking with other, institutions deploying Galaxy locally?

2012-05-02 Thread Sarah Maman
Hello, This is a great idea. I'm interested. Thanks ! Sarah Maman -- Message: 1 Date: Fri, 27 Apr 2012 13:45:16 -0500 From: Ann Black-Ziegelbein annbl...@eng.uiowa.edu To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev

[galaxy-dev] MarkupSafe cannot be fetched

2012-04-27 Thread Sarah Maman
in the cloud (https://main.g2.bx.psu.edu/). For example, Visualization menu is absent and I think it should be related to the previous warning? How to ensure that eggs be properly fetched? Thank you in advance, Sarah Maman ___ Please keep all

[galaxy-dev] Galaxy version / Mercurial

2012-04-25 Thread Sarah Maman
in order to use, in the future, Mercurial and hg pull to update Galaxy version. Thanks a lot, Sarah Maman ---BeginMessage--- Hello, I would like to get source code with Mercurial of this tarballs : galaxy-dist.b258de1e6cea.tar.gz, and not the latest source. Is it possible to specify

Re: [galaxy-dev] Galaxy version / Mercurial

2012-04-25 Thread Sarah Maman
Thank you very much Dannon, it works. The more I discover Galaxy, the more I appreciate its use. Again, thank Galaxy team for this great tool. Sarah Maman Dannon Baker a écrit : Hi Sarah, You should be able to do this with the -r option of the clone command, so: `hg clone -r b258de1e6cea

[galaxy-dev] Display galaxy variable

2012-03-09 Thread Sarah Maman
Hello, In a Galaxy tool, I would like to display a pre-completed path in the xml inputbox, inside the tool.xml file. Consequently, I would like to add a variable in an param value= / tag , like this : tool id=test name=test version= command interpreter=shtest.sh $in $out/command inputs

Re: [galaxy-dev] LDAP authentification

2012-02-17 Thread Sarah Maman
be better for security. Faithfully, Sarah Maman Nate Coraor a écrit : On Feb 13, 2012, at 7:38 AM, Sarah Maman wrote: Hello, I managed to connect to Galaxy to LDAP ;-) Three points were blocking for me: * Being root of my virtual machine can carry out tests * I confused login / password of two

Re: [galaxy-dev] LDAP authentification

2012-02-13 Thread Sarah Maman
Hello, I managed to connect to Galaxy to LDAP ;-) Three points were blocking for me: * Being root of my virtual machine can carry out tests * I confused login / password of two LDAP, so I thought that my authentication method was not good while I was using the wrong password ... * It is better

[galaxy-dev] Adding a new python tool

2012-02-07 Thread Sarah Maman
Hello, I managed to add a new tool coded in bash but I am having some difficulty adding a tool coded in python. Here are the contents of the test files: * Content of test.xml file in galaxy/galaxy-dist/tools/test/test.xml : tool id=test name=Test name descriptionTest description/description

Re: [galaxy-dev] LDAP authentification

2012-01-31 Thread Sarah Maman
, *use_remote_user = True* and *remote_user_maildomain = toulouse.inra.fr* Thanks in advance, Sarah Nate Coraor a écrit : On Jan 19, 2012, at 10:49 AM, Sarah Maman wrote: Hi Brad, Hi Christopher, Thanks a lot. I'm talking to Open LDAP. I have changed RequestHeader set REMOTE_USER

[galaxy-dev] Unix user account/connection and Galaxy connection

2012-01-30 Thread Sarah Maman
Dear all, There is currently no link between an user ssh connection on his own account (own space on Unix) and the Galaxy connection. How to run Galaxy on an Unix user account? How to link the data storage system and the Unix user account (symlink?)? The goal is to not need to copy or move

[galaxy-dev] LDAP authentification

2012-01-19 Thread Sarah Maman
. This is generally due to a misconfiguration in the upstream server. Thank you, and best regards Sarah Maman ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other

Re: [galaxy-dev] LDAP authentification

2012-01-19 Thread Sarah Maman
Hi Brad, Hi Christopher, Thanks a lot. I'm talking to Open LDAP. I have changed RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e to RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e But I always have the same message /(Access to Galaxy is denied Galaxy is configured to authenticate users

[galaxy-dev] Information about server availability

2012-01-05 Thread sarah Maman
will be available ? Please, excuse me if this information is available on your web and if I have not seen it. Happy new year, Sarah Maman -- Sarah Maman INRA - LCG - SIGENAE Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Tax