- galaxy-dev - lists.galaxyproject.org

heatmap capabilities!
by Hakeem Almabrazi 11 Apr '13

11 Apr '13

Hi, Is there a heatmap tool for Galaxy? If so can someone send me a link to how to integrate it to a local galaxy? I appreciate your help.

2 1

Dataset diskspace useage
by Alexander Kurze 11 Apr '13

11 Apr '13

Hello, I am running a local galaxy server where I have restricted the amount of data for each user to a 100gb. Users are able to delete their own history to regain diskspace. However, for some users deleting the histories (all saved histories and datasets) only frees ~80% of their allowance. As an admin I ran the "clean-up" scripts which were recommended on the galaxy homepage. But this still didn't increase their data limit. Anyone knows what is going on? Best wishes, Alex

2 1

negative user data usage
by Geert Vandeweyer 11 Apr '13

11 Apr '13

Hi, Today, I found out that one user in our local galaxy installation (the administrator user) has a negative disk usage. - Reports shows : -72780720701 bytes - Galaxy history shows: -1% Does anybody have suggestions on what might be causing this and how to solve it? There is about 660 Gb of data in the histories of that user, but it was more before. I believe it happened after some histories were deleted and there was a message of one of them being shared. Best, Geert -- 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.vandeweyer(a)ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

3 2

Tophat didn't run
by Sarah Maman 11 Apr '13

11 Apr '13

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. / Tool execution generated the following error message: Error in tophat: [2013-04-10 09:17:07] Beginning TopHat run (v2.0.5) ----------------------------------------------- [2013-04-10 09:17:07] Checking for Bowtie Bowtie version: 2.0.0.7 [2013-04-10 09:17:07] Checking for Samtools Samtools version: 0.1.19.0 [2013-04-10 09:17:07] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/work/galaxy/Danio_rerio.Zv9.62.dna.chromosome.22.fa.*.bt2) The tool produced the following additional output: TopHat v2.0.5 tophat -p 4 /work/galaxy/Danio_rerio.Zv9.62.dna.chromosome.22.fa /work/galaxy/database/files/006/dataset_6528.dat [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file. Epilog : job finished at mer. avril 10 09:17:12 CEST 2013 / In this post (http://dev.list.galaxyproject.org/tophat-for-illumina-looking-in-wrong-dire…) the solution isn't found. Do you have any idea, 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 --*--

2 3

Setting extension of file names generated by Galaxy
by Holtgrewe, Manuel 11 Apr '13

11 Apr '13

Dear all, is it possible to make Galaxy use a specific extension for a given data type without a wrapper? I.e. can I make Galaxy use the extension .bam, .sam, .fasta etc. internally instead of .dat? Thanks, Manuel

2 1

"Local install" of Galaxy Tool
by Holtgrewe, Manuel 11 Apr '13

11 Apr '13

Dear all, I am trying to follow the Admin Add Tool Tutorial [1]. I put my binary BINARY into the location ${galaxy_root}/tools/${category}/BINARY. However, it is not found using if the <command> tag looks as follows: <command>BINARY (arguments)</command> When I put the following, it works: <command>$__root_dir__/tools/CATEGORY/BINARY</command> Am I doing something wrong? Is there a preferable way to such a "local" installation than my second try? Thanks! Manuel [1] http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial

2 5

adding datatypes in tool xml
by Robert Baertsch 10 Apr '13

10 Apr '13

If I want to add a new datatype during tool installation from the shed, how define that in the tool.xml? Is this documented anywhere? -Robert

3 2

How can I creating a tool in C++
by Ramon Tiburski 10 Apr '13

10 Apr '13

Hi,I need to create a new tool in c++, but I'm with a lot of difficult to link the cpp or exe (I don't know) with the xml document. Can you help me with an example that receives a txt file with a phrase and shows another txt file without the spaces of this phrase? Thanks

2 1

Why Galaxy? What the advantages?
by Ramon Tiburski 10 Apr '13

10 Apr '13

I started studying the galaxy and would like to know about the power of this tool, you could tell me why using the galaxy and what are its advantages compared to other similar systems. And another question, can I adapt galaxy to another area like the agronomy, only with creating new tools? Thanks

2 1

Bowtie2 and Tophat2 versions
by Lance Parsons 10 Apr '13

10 Apr '13

I noticed that the latest versions for Bowtie2 and Tophat2 listed on the Tool Dependencies page (http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies) are 2.0.4 for Bowtie2 and 2.0.6 for Tophat2. Are these the latest supported versions? Does anyone know if it's advisable to go with the latest (Bowtie2 2.1.0 and Tophat 2.0.8) with Galaxy? I'm looking forward to these tools being moved to the ToolShed so updates to the underlying tools are accompanied by Galaxy tool version updates, but until then I'm just trying to make sure my users can use the latest versions that are compatible. Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

2 1