[galaxy-user] Text Manipulation > Compute > c1[1:c1.find("(")] fails

Folks, I have a column c1 that has entries like "GXP_297346(PVALB/human)". I'm trying to use Text Manipulation > Compute to strip off the "(...)" portion, leaving only the accession (which can vary in length). I have tried a variety of things that work in my python command line, but fail here,

[galaxy-user] How to re-use a parameter in a workflow?

Galaxy Users, I have a workflow where I'd like the user to input a value once, say a number of nucleotides. That value would then be used as an input parameter to several different tasks, for example, to two instances of "Operate on Genomic Intervals > Get flanks" , where it would be used both

Re: [galaxy-user] Error running cufflinks on Galaxy

Jen, We are running into the same problem on our local install of galaxy. We're running Cufflinks v.1.0.1, on a BAM file (accepted_reads) from TopHat run on mm9 based RNAseq data (paired-end 25mer), and pulled down the changes made to galaxy last month to support the 1.0.1 version of Cufflinks

[galaxy-user] FTP and command line access in Galaxy

Nate, The Galaxy's ability to pull files with user/password from FTP sites as a client is great. However, I need to pull data from an HTTP site at a sequencing center with user/password (already tried to get them to set up an FTP server, no luck). Any way to do this? If not, would it be

[galaxy-user] working collaboratively in a history: How To?

Jen, Thanks for all your quick responses. I have found Googling documentation for Galaxy extremely hard, because it is such a common term. How I wish it had been misspelled (intentionally)! I work in an informatics core, where several of us collaborate on projects. We have a local Galaxy ins

Re: [galaxy-user] can I merge histories?

tory with my source data, and copy it into my working histories, but doesn't seem to work for merging histories. Regards, Curtis -Original Message- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Tuesday, June 14, 2011 11:53 AM To: Robert Curtis Hendrickson Cc: 'g

[galaxy-user] can I merge histories?

Folks, Is there some way I can merge histories? I ran a workflow on 3 different samples in one history, each time putting them in a different history with the same name. However, Galaxy created 3 new histories, each with the same name! But I need the data in the same history to compare and con

Re: [galaxy-user] UCSC->EMBOSS/fuzznuc->UCSC workflow?

u] > Sent: Wednesday, May 18, 2011 11:45 AM > To: Robert Curtis Hendrickson > Cc: galaxy-user > Subject: Re: [galaxy-user] UCSC->EMBOSS/fuzznuc->UCSC workflow? > > Hello Curtis, > > The BED extraction data can be resolved in Galaxy. Pull out the whole > gene and t

Re: [galaxy-user] UCSC->EMBOSS/fuzznuc->UCSC workflow?

will allow me to do that last conversion step. http://main.g2.bx.psu.edu/u/curtish-uab/h/fuzznuc Any advice would be appreciated. Curtis > -Original Message- > From: Jennifer Jackson [mailto:j...@bx.psu.edu] > Sent: Wednesday, May 18, 2011 11:45 AM > To: Robert Curtis He

Re: [galaxy-user] UCSC->EMBOSS/fuzznuc->UCSC workflow?

From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Monday, May 16, 2011 6:50 PM To: Robert Curtis Hendrickson Cc: 'galaxy-user@lists.bx.psu.edu' Subject: Re: [galaxy-user] UCSC->EMBOSS/fuzznuc->UCSC workflow? Hello Curtis, The coordinates of your match are with respe

[galaxy-user] UCSC->EMBOSS/fuzznuc->UCSC workflow?

Folks, I wanted to scan the 2kb upstream of a list of human gene isoforms for TFBS using fuzznuc. I was able to "Get Data"> "UCSC Main" > "As sequence" and get my sequences "EMBOSS" > fuzznuc ran fine, and output the hits HOWEVER, fuzznuc lost the genomic position information that UCSC has put