[galaxy-dev] Error Setting Up Local Galaxy Server

that I can start an instance on my computer. Any advice on how to deal with this problem would be much appreciated. Thank you for taking the time to read this email, Kevin Chang ___ Please keep all replies on the list by using "reply

[galaxy-dev] Problem Running TopHat2

made sure that the samtools do appear to be installed since they can be found listed under "Managed Installed Tool Shed Repositories". Is it possible that they were installed incorrectly? Any help is much appreciated. Thanks for taking the time to read this, Kevin Chang

Re: [galaxy-dev] Problem Running TopHat2

appears that installing the samtools themselves did not fix the problem. Are there any other ways to try and fix this problem? Thanks for taking the time to help me out, Kevin Chang Sent from Windows Mail From: Alper Kucukural Sent: ‎Tuesday‎, ‎August‎ ‎26‎, ‎2014 ‎1‎:‎21‎ ‎PM To: Kevin Cc: galaxy-dev

Re: [galaxy-dev] Problem Running TopHat2

be concerned about? Or is it okay to proceed without the metadata being completely done? I intend to use this accepted hits file for Cufflinks and Cuffdiff later on. Thanks for all your help, Kevin Chang Sent: ‎Friday‎, ‎August‎ ‎29‎, ‎2014 ‎10‎:‎52‎ ‎AM To: Kevin Cc: galaxy-dev@lists.bx.psu.edu

Re: [galaxy-dev] Problem Running TopHat2

Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found Thanks, Kevin Chang From: Alper Kucukural Sent: ‎Friday‎, ‎August‎ ‎29‎, ‎2014 ‎10‎:‎16‎ ‎AM To: Kevin Cc: galaxy-dev@lists.bx.psu.edu What was the error? From: Kevin <chang...@byramhills.net&g

Re: [galaxy-dev] best practice for data matrices with metadata

I am wondering if the biohdf project is a good way to keep the meta data. Cheers Kevin On 17-Feb-2011, at 5:11 AM, Keith Sheppard wrote: Hi All, I'm working on building some galaxy tools which can be used together in a workflow and one data structure that seems to show up a lot is a

[galaxy-dev] dead link

The link for datasets is dead:  http://screencast.g2.bx.psu.edu/usinggalaxy_datasets/flow.html thanks, Kevin___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Gal

[galaxy-dev] Problem with the "set_library_permissions" function on bioblend

in=[admin_id], manage_in=[admin_id]) 3 --> Moreover,are we supposed to view the content of this page?http://localhost:8080/api/libraries/417e33144b294c21/permissions -- Thank you in advance to the community for your help, Kevin MURET Intern at

Re: [galaxy-dev] Problem with the "set_library_permissions" function on bioblend

Error Internal Server Error The server has either erred or is incapable of performing the requested operation. WSGI Server I never success running the allocation of permissions. Thank you for your help, Kevin MURET Intern at Station Biologique de Roscoff ABiMS platform

Re: [galaxy-dev] Problem with the "set_library_permissions" function on bioblend

axy/galaxy4kevin/galaxy-dist/lib/galaxy/model/__init__.py", line 1960, in to_dict rval[ 'root_folder_id' ] = 'F' + rval[ 'root_folder_id' ] TypeError: cannot concatenate 'str' and 'int' objects Kevin MURET Intern at Station Biologique d

[galaxy-dev] missing .fa files in rsync datacache indexes

fasta? Thanks, Kevin. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

Re: [galaxy-dev] missing .fa files in rsync datacache indexes

Thanks Dave, A question before we go ahead, why are they missing in the first place? Does the main galaxy not actually need them? are the tools moving away from fa? Cheers, Kevin. On Tue, Sep 25, 2012 at 11:12 PM, Dave Bouvier wrote: > Kevin, > > Correct, converting from 2bit

Re: [galaxy-dev] missing .fa files in rsync datacache indexes

. All feedback/contributions are welcome! Kevin On Wed, Sep 26, 2012 at 11:26 PM, Dave Bouvier wrote: > Kevin, > > We decided to exclude fasta files mainly because 2bit is a lossless > compression with a much lower file size, so it would be a waste of our > users' bandwidth and

[galaxy-dev] Gencode Partition (version 1.0.0)

x.php/Collecting_Feature_Sets_from_All_Analysis_Groups Any idea where I can find the proper documentation? or should I contact the people behind http://genome.imim.es/ ? Thanks, Kevin ___ Please keep all replies on the list by using "reply al

[galaxy-dev] language inside tag set

Hi, I'm looking for documentation on what I can do inside the tag for tools. I know of things like #if str( $input ) == 'yes': Do stuff #end if can I do for loops? What should I google? I can't find anything on the

[galaxy-dev] How to make toolshed tool to create dummy env.sh

r it to be sourced? Ideally I would be elegant if there is a way to create this env.sh easily as it's the best way for a galaxy admin to manage the different versions of dependencies. Thanks, Kevin. ___ Please keep all replies on the list by u

Re: [galaxy-dev] How to make toolshed tool to create dummy env.sh

er for the toolshed tool to create these rather than the admin. Cheers, Kevin. On 13 November 2012 12:36, Derrick Lin wrote: > Hi Greg, > > I am wondering the similar thing. If I understand Kevin's post correctly, I > think the question really is: if the automated tools buil

[galaxy-dev] My fix for error during EMBOSS toolshed install

tool installed fine Kevin. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

Re: [galaxy-dev] Barcode/adapter/primer trimming/filtering of sequences/reads

Have you looked at http://code.google.com/p/cutadapt/ Features - Gapped alignment with mismatches and indels, that is, errors in the adapter are tolerated - Finds adapters both in the 5' and 3' ends of reads - Accepts FASTQ, FASTA or .csfasta and .qual files (for AB SOLiD data) - An