Re: [galaxy-user] Problem with bam and/or bai files

Hi Mike, Someone from the Galaxy team can perhaps give some insight on what went wrong, I can comment on the error message from IGV. That error is thrown from Picard, in every case I've investigated so far it was traced to a problem with the index. The most common causes are (1) a problem

[galaxy-user] Problem with bam and/or bai files

Hello Galaxy Team,   I have been using Galaxy for SNP detection for with great success. Basically, I followed the screen-cast from Anton without any problems. The only change was to use the BWA instead of Bowtie. Until now, I have always assigned my raw read files to the hg19 format. Now I want

Re: [galaxy-user] cluster install

It's reasonably easy to set up Galaxy to use external authentication. We modeled our authentication after the way MSI folks did it as posted on the galaxy-dev list a while ago. We use SSO (Single Sign On) with mod_auth_tkt SSO tied into an LDAP back-end used for our cluster. I'd be happy to shar

[galaxy-user] cluster install

Dear Galaxy - We would like to install and instance of Galaxy on our campus cluster. The install process looks very straight forward, but tying it in with our authentication system for the current, functioning cluster may not be as simple. It appears that galaxy is easy to install if there a

[galaxy-user] cluster install

Dear Galaxy - We would like to install and instance of Galaxy on our campus cluster. The install process looks very straight forward, but tying it in with our authentication system for the current, functioning cluster may not be as simple. It appears that galaxy is easy to install if there are l

[galaxy-user] Genome database/builds missing?

I've been using galaxy to analyze maf files and today the drop down list for database/builds for genomes has lost most of the genomes once listed. I no longer see any bacteria or plants on the list, specifically TAIR9 arabidopsis is no longer on the drop down list when it was just yesterday. Di

[galaxy-user] get data through FTP site

Hello, I uploaded (on Oct, 25) data through FTP site and I was not able to retreiven them to include them in a history. I suppose that the files should appeared in the FTP list under the Get data page. THese data are named "P2 fastq .gz" files that I wold like to use in RNA Seq workflow. Th

Re: [galaxy-user] permanently delete problem

Great, thanks for letting us know. Richard Mark White wrote: > actually, i just waited a bit and now they are deletd. > r > > > > > > From: Nate Coraor > To: Richard Mark White > Cc: GANDRILLON OLIVIER ; > "galaxy-u...@bx.psu.edu" > Sent: Wednesday, October

[galaxy-user] sample for video for example 3 in ngs analyses in galaxy

Hi, I am watching the video 'Example 3 - mapping paired-end Illumina run and visualizing results at UCSC Browser', and would like to try out the exercise. I don't have paired-end Illumina fastq sample, Could you provide me th

Re: [galaxy-user] permanently delete problem

actually, i just waited a bit and now they are deletd. r From: Nate Coraor To: Richard Mark White Cc: GANDRILLON OLIVIER ; "galaxy-u...@bx.psu.edu" Sent: Wednesday, October 26, 2011 12:55 PM Subject: Re: permanently delete problem Richard Mark White wrote:

Re: [galaxy-user] permanently delete problem

Richard Mark White wrote: > hi, >   so i went to options-->saved history-->advanced-->deleted datasets.  then > checked all of them, and then hit "permanently delete". > but nothign happened.  they still show up as deleted, and they are taking up > lots of my quota. > how do i get rid of these? >

Re: [galaxy-user] Names for genes in RNA-Seq analysis

Regarding the GTF files for cuffllinks, how do I obtain one for all human mRNA that actualy contains gene names rather than accession numbers. I went to the UCSC table browser but their files contain accession numbers that I dont know how to decode en-masse.

[galaxy-user] permanently delete problem

hi,   so i went to options-->saved history-->advanced-->deleted datasets.  then checked all of them, and then hit "permanently delete". but nothign happened.  they still show up as deleted, and they are taking up lots of my quota. how do i get rid of these? rich _

Re: [galaxy-user] Names for genes in RNA-Seq analysis

Dear Carl After having solved a couple of other problems, I am now to the point where I can: 1.either get the FKPM and no names or 2. have the names and FKPM values to zero (or "OK" ?) So I was wondering whether you had solved this FKPM value problem with chicken you had? Best Olivier Le 26/

Re: [galaxy-user] Over disk quota

GANDRILLON OLIVIER wrote: > Hello > > I just received the following message while using Galaxy through the web > > "You are over your disk quota. Tool execution is on hold until your disk > usage drops below your allocated quota." > > I deleted a couple of files but it didn't helped. > I checke

Re: [galaxy-user] reducing size on disk to comply with quotas

Patrick Kenneth Gonzales wrote: > Hi, I am currently using 636gb of storage and would like to reduce it. I have > deleted (from disk) most of the datasets in my history. All I've kept are the > Bam files which are around 2.7gb each . Unfortunately, the "size on Disk" > reads 448.5gb in my saved

Re: [galaxy-user] Cistrome

Hello Albena, The Cistrome team should be contacted directly at: http://cistrome.org/ cistrome-b...@jimmy.harvard.edu Thanks, Jen Galaxy team On 10/25/11 5:08 PM, Albena Pramatarova, Dr wrote: Hi What is the procedure for getting a username and password key to use the Aspera tool? Tha

[galaxy-user] reducing size on disk to comply with quotas

Hi, I am currently using 636gb of storage and would like to reduce it. I have deleted (from disk) most of the datasets in my history. All I've kept are the Bam files which are around 2.7gb each . Unfortunately, the "size on Disk" reads 448.5gb in my saved histories window. It is my understanding

[galaxy-user] Over disk quota

Hello I just received the following message while using Galaxy through the web "You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota." I deleted a couple of files but it didn't helped. I checked the FAQ and could not get the answer. Tha

[galaxy-user] Cistrome

Hi What is the procedure for getting a username and password key to use the Aspera tool? Thank you for your help. Albena ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server