Re: [galaxy-dev] Gal-Cloudman AMI Fails

John, I'm still working on figuring out who created the AMI you're running across (it isn't under the main Galaxy cloud account, see the '072133624695' in the name string), but for future reference we'll always keep the recommended AMI to use listed on usegalaxy.org/cloud. At this point, it's

[galaxy-dev] Gal-Cloudman AMI Fails

Hello GalFolks- I saw a new galaxy-cloudman AMI appear ( 072133624695/galaxy-cloudman-2012-02-26 ) and was interested in giving it a whirl. But when I tried to launch it got the following error: """ The requested instance type's architecture (x86_64) does not match the architecture in the manifes

Re: [galaxy-dev] [galaxy-user] Problem using Galaxy on the cloud

Jan; Glad to hear you got Galaxy running successfully. It sounds like everything is good to go once we sort out the disk space issue. > > However, when I try to use NX to get the virtual desktop going I get the > > message usr/bin/nxserver: line 381: echo: write error: No space left > > on device

Re: [galaxy-dev] HMMER wrappers

On Tuesday, March 6, 2012, Edward Kirton wrote: > i gave it a bad name previously and peter didn't find it in a > search at first, but i couldn't change the name, so i created > a new repository. i put a note in the old repo (hmmscan), > referring to the new repo (hmmer). that may suffice. howev

Re: [galaxy-dev] [galaxy-user] Problem using Galaxy on the cloud

Hi Jan, Since this question is about a Cloud installation, I am going to forward your question over to the galaxy-...@bx.psu.edu mailing list so that the development community will have a better chance of seeing it and providing feedback. http://wiki.g2.bx.psu.edu/Support#Mailing_Lists Thank

Re: [galaxy-dev] [galaxy-user] Advice on disabling SGE queue on galaxy-cloudman

Hi John, Since this question is about a Cloud installation, I am going to forward your question over to the galaxy-...@bx.psu.edu mailing list so that the development community will have a better chance of seeing it and providing feedback. http://wiki.g2.bx.psu.edu/Support#Mailing_Lists Than

Re: [galaxy-dev] bacterial genomes missing?

Hi Dan: When I look at builds.txt I see only the eukaryotic genomes... the canary that triggered my investigation was eschColi_K12. It used to be present, but is now not in builds.txt it is present in ucsc_build_sites.txt When i go to the xml at ucsc's test server http://genome-test.cse.ucsc.e

Re: [galaxy-dev] bacterial genomes missing?

Hi Brad, I just ran the updateucsc.sh script and it seemed to work correctly. Can you be more specific as to which builds you are missing and could you try running the script again and if it doesn't work, copy the log output here? Thanks for using Galaxy, Dan On Mar 6, 2012, at 12:15 PM, La

Re: [galaxy-dev] HMMER wrappers

i gave it a bad name previously and peter didn't find it in a search at first, but i couldn't change the name, so i created a new repository. i put a note in the old repo (hmmscan), referring to the new repo (hmmer). that may suffice. however you folks how you want to handle it is fine. On Tue,

Re: [galaxy-dev] Possible Galaxy memory leak?

We've experience memory-leak symptoms and we also use the PBS job runner here. We did not try to locate the leak, but instead installed monit as a work-around http://mmonit.com/monit/ Todd Oakley On 3/6/2012 11:10 AM, Nate Coraor wrote: There is also a memory leak that occurs when using the

Re: [galaxy-dev] [galaxy-user] Getting errors trying to enable samtools_mpileup

On Mar 1, 2012, at 8:49 AM, Waldron, Michael H wrote: > I am running a local copy of Galaxy, last ran 'hg pull -u' on 2/20/12. > > I am trying to enable use of Mpileup for SAM Tools, and have added the entry > for the samtools_mpileup.xml file in tool_conf.xml. However, when I startup > Galaxy,

Re: [galaxy-dev] Potential issue with eggs ?

On Feb 29, 2012, at 11:50 AM, Michael Burrell (TOC) wrote: > Good evening all, > > I am seeing the following issue when attempting to start galaxy. > > Traceback (most recent call last): > File "./scripts/paster.py", line 34, in > command.run() > File > "/home/home/galaxy/software/ga

Re: [galaxy-dev] Possible Galaxy memory leak?

There is also a memory leak that occurs when using the pbs job runner. I believe the leak is somewhere in libtorque or pbs_python but I have not yet tracked it down. --nate On Feb 29, 2012, at 3:28 PM, John Chilton wrote: > We had intermittent issues like this for an embarrassingly long time

Re: [galaxy-dev] uploading multiple files into one dataset

On Feb 29, 2012, at 11:34 AM, Jorrit Boekel wrote: > Dear list, > > Our lab's proteomics data is frequently outputted into >50 files containing > different fractions of proteins. The files are locally stored and not present > on the Galaxy server. We've planned to somehow (inside galaxy) merge

Re: [galaxy-dev] Variable number of inputs in Workflow (or optional inputs)

This seems to fall within the recent discussion of map/reduce operators for workflows, e.g. breaking large jobs up for embarrassingly parallel tasks, then merging them back at some later point. Dannon mentioned some basic functionality does exist within Galaxy to do this, but it's at an early s

[galaxy-dev] bacterial genomes missing?

It seems that the bacterial genomes that used to come from ucsc via update_ucsc.sh are now gone... Has anybody else observed this? Fixed it? Brad -- Brad Langhorst langho...@neb.com 978-380-7564 ___ Please keep

Re: [galaxy-dev] NFS, Cluster and working directories questions

On Feb 28, 2012, at 9:24 AM, Louise-Amélie Schmitt wrote: > Hello, > > We're currently trying to switch to a big cluster but we have a lot of doubts > and questions, especially since the I/O is a serious issue for our NFS. > > - We saw the outputs_to_working_directory option in the .ini file,

Re: [galaxy-dev] can the sample tracking system transfer (copy) data to a dataset library not in private Galaxy server data directory tree and then just link files?

On Feb 27, 2012, at 4:09 AM, Leandro Hermida wrote: > Dear all, > > Is there a way with the Galaxy sample tracking system to have the > dataset transfer feature copy data to a dataset library outside the > private Galaxy server data directory tree and then the dataset library > just link (like yo

Re: [galaxy-dev] [galaxy-user] Data not uploading in Local instance

Hi Luciano, I've moved this over to galaxy-dev since it concerns a local installation. On Feb 26, 2012, at 6:19 PM, Luciano Cosme wrote: > I have python 2.7 and it seems to be the problem with it. Just formated the > partition I had linux and fresh install everything and still have same > pro

Re: [galaxy-dev] Variable number of inputs in Workflow (or optional inputs)

Good Morning, We are also interested in this capability. To give a concrete example, we sometimes receive multiple sequence runs 1Š* for the same sample. We would like to be able to process each run of the sample through BWA and then merge them together, post process it a bit, and then send th

[galaxy-dev] Problems getting galaxy to start

Good evening, I am having difficulty getting galaxy to startup over the last couple of days, I initially suspected that it was an issue with the eggs, but have replaced these and the following errors remain, galaxy@jic55119: $ python --version Python 2.6.6 galaxy@jic55119:galaxy-central$ ./run

[galaxy-dev] large ftp uploads to galaxy cloud

I'm having difficulty uploading files > 6GB or so to an EC2 instantiation of galaxy cloud. The size seems to correlate with the amount of space available on the root volume. I can upload a 5.06 GB file but any larger and it never shows up in the galaxy upload history. I'm using a "Large" EC2

Re: [galaxy-dev] Using complete workflow in another workflow

This is definitely something we're looking to implement in Galaxy. I started working on a proof of concept a while back for boxing workflows up as tools, but I have not had a chance to finish it yet. What Thon suggests in terms of a simple copy/paste is interesting, and probably a far simpler

Re: [galaxy-dev] Using complete workflow in another workflow

Hello - I would also like the +1 this feature. I currently use the "clone" feature of a workflow to make a copy and modify, but if I change the original workflow, I think have to remember which workflows I cloned into and hand modify them as well. If we had the ability to re-use workflows, then

Re: [galaxy-dev] HMMER wrappers

Hi Ed, Do you want the hmmscan repository itself deleted? It's been downloaded / cloned 86 times, although it is never been automatically installed into a local Galaxy since the contained tool does not properly load into Galaxy. We generally do not like to delete things like this because doin

Re: [galaxy-dev] Variable number of inputs in Workflow (or optional inputs)

Hi Daniel, My apologies! I misunderstood what your question was about. You are correct, the required inputs are defined when the workflow is created. For tools that accept a variable number of inputs, when that tool is added to a workflow, the run-time parameters, including expected inputs, a

Re: [galaxy-dev] Variable number of inputs in Workflow (or optional inputs)

Hello Daniel, I had the same problem when I started to work with Galaxy workflows. My workaround is: 1) Modify the first tool of the workflow Make it work on a simple text file that contains a list of input file paths (one by line) instead of several files. 2) Create a galaxy tools that can

Re: [galaxy-dev] Variable number of inputs in Workflow (or optional inputs)

Hi Jennifer, Thanks for the reply. However, my question was not about building tools. My question was about building a workflow (using the workflow editor with existing tools), as a user of galaxy. Using the workflow editor, when I create a workflow using a tool that allows a variable number of