[galaxy-dev] Reload a tool from the command line

2011-09-27 Thread Jean-Baptiste Denis
Hello evyerbody, i guess this question has already been answered, but i didn't find any :/ Is there a way to reload a tool file from the command line ? I'd like to automate the process when a user upload a new version of an existing tool. Am I reinventing the wheel here, is there something

Re: [galaxy-dev] EST download from any source?

2011-09-27 Thread Nate Coraor
Timothy Wu wrote: On Thu, Sep 15, 2011 at 5:32 PM, Timothy Wu 2hug...@gmail.com wrote: On Thu, Sep 15, 2011 at 4:58 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Thu, Sep 15, 2011 at 9:32 AM, Timothy Wu 2hug...@gmail.com wrote: I think I need some kind of data source

Re: [galaxy-dev] conversion of fastq files

2011-09-27 Thread Nate Coraor
mallika V wrote: hi I am very new to the galaxy software. I have to convert one fastq file of nearly 5 gb size and unable to do that. i tried to install galaxy in locally but it tells some eggs are out of date. Can anyone plz help me in this regard Hi, With respect to the public version of

Re: [galaxy-dev] MergeSamFiles.jar and TMPDIR

2011-09-27 Thread Nate Coraor
Glen Beane wrote: We recently updated to the latest galaxy-dist, and learned that the sam_merge.xml tool now uses picard MergeSamFiles.jar to merge the files instead of the samtools merge wrapper sam_merge.py. this is a problem for us because MergeSamFiles.jar does not honor $TMPDIR when

[galaxy-dev] Bug importing from data library to history

2011-09-27 Thread Lance Parsons
I'm running a local instance of Galaxy that has been working quite well. However, I've recently run into a problem when importing datasets from a data library into a history. The Size on Disk of the history grows by the size of the imported dataset, however, the new dataset is not visible

Re: [galaxy-dev] prevent downloaded files with .txt added

2011-09-27 Thread David Hoover
I apologize for responding to my own email, but I thought others might want to know. This turned out to be a Safari-dependent problem. Lots of other people have complained, but there doesn't seem to be any direct fix. My quick solution was to make sure the downloaded file is gzipped. This

Re: [galaxy-dev] HOW TO RETRIEVE DATA FROM HISTORY??!!

2011-09-27 Thread Matthew Conte
Hi Greg, Has Steve's gls script made it into ~/contrib of the Galaxy distribution? I'd love to try it out as I'm having issues with the helper.py script giving me false IDs. Thanks, Matt On Fri, Sep 2, 2011 at 9:18 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Steve, Thanks for making