Re: [galaxy-dev] (no subject)

2013-05-06 Thread sridhar srinivasan
HI, Thanks for the reply. actually my server is not connected with the internet. Previously i downloaded in another system with internet connection and installed to server. now i gave internet connection to the server now i could connect to it and download the python eggs. Thanks Sridhar On

Re: [galaxy-dev] Tool Shed Request - sanity check uploads?

2013-05-06 Thread Peter Cock
On May 2, 2013, at 12:54 PM, Peter Cock wrote: Another even simpler change (which would also make a big difference) is to actually have the name of the current repository on the Upload a single file or a tarball page. Thanks, On Thu, May 2, 2013 at 9:32 PM, Greg Von Kuster g...@bx.psu.edu

Re: [galaxy-dev] Missing test results on (Test) Tool Shed

2013-05-06 Thread Peter Cock
On 2013-05-01 08:52, Greg Von Kuster wrote: Hi Peter, I created the following Trello card for this and things will be fixed as a priority. Thanks for letting us know! https://trello.com/card/toolshed-issues-with-functional-test-results/506338ce32ae458f6d15e4b3/823 On Wed, May 1, 2013 at

Re: [galaxy-dev] user creation using API

2013-05-06 Thread Rémy Dernat
Hi, This is an old topic now, but here is a little update (fork from Git / John Chilton) of this code: https://gist.github.com/remyd1/5524162 Regards Remy 2013/1/8 Hagai Cohen haga...@gmail.com This is really helpful, Works great. Thanks, Hagai On Mon, Jan 7, 2013 at 5:13 PM, John

Re: [galaxy-dev] Missing test results on (Test) Tool Shed

2013-05-06 Thread Dave Bouvier
Peter, Yes, there are a few issues that are causing some repositories not to be tested correctly. I've discovered the problem, but the solution will require a bit of work. My goal is to have this resolved as soon as possible. --Dave B. On 5/6/13 05:10:57.000, Peter Cock wrote: On

[galaxy-dev] May 2013 Galaxy Update

2013-05-06 Thread Dave Clements
Hello all, The May 2013 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_05 . *Highlights:* - the GCC2013 http://wiki.galaxyproject.org/GalaxyUpdates/2013_05#GCC2013 *early registration deadline is 24

[galaxy-dev] Taxonomy fetching not working

2013-05-06 Thread Deepthi Thomas Kannanayakal
Hi Galaxy team, I am having problems with taxonomy information fetching.(Metagenomic Analysses-Fetch taxonomic representation). According to the following link http://dev.list.galaxyproject.org/quot-Fetch-taxonomic-representation-quot-DOESN-T-WORK-td4565489.html I have installed libraries from

[galaxy-dev] LWR runner configuration for shared folder in cluster

2013-05-06 Thread Krampis, Konstantinos
Hi all, I am trying to set up a Galaxy cluster using the LWR runner. The nodes have a shared filesystem and in universe.wsgi this parameter is set : job_working_directory = /mnt/shared ... clustalw = lwr://http://192.168.33.12:8913 this folder has been chown-ed to the galaxy user, and

Re: [galaxy-dev] LWR runner configuration for shared folder in cluster

2013-05-06 Thread John Chilton
Hello Dr. Krampis, At the present, the LWR is most valuable when there is not a shared file system between the server executing the jobs and the server hosting Galaxy. In this case you seem to have a shared filesystem so I would think setting up something like sun grid engine to manage the jobs

Re: [galaxy-dev] Any hint on how to use Galaxy within virtualenv?

2013-05-06 Thread Jean-Francois Payotte
Hi Dannon, We did update our galaxy development instance to the latest distribution (April 1st). Unfortunately, because of some LDAP issue (we are testing to implement LDAP authentication at the same time) I didn't had time yet, to test if this would solve the markupsafe issue. As soon as I

Re: [galaxy-dev] LWR runner configuration for shared folder in cluster

2013-05-06 Thread Krampis, Konstantinos
Hi John, thanks for the quick reply! It is actually a virtual cluster using virtual machines with VirtualBox, which are brought up via Vagrant (www.vagrantup.com) - that also sets up the shared filesystem. I chose LWR for the reason that it not a real cluster, and needed something lightweight

Re: [galaxy-dev] galaxysession cookie secure flag

2013-05-06 Thread Vipin TS
Hello, I figured out the place where the cookie gets set in Galaxy and then add secure to that. Apache configuration didn't work well. added the following code into function set_cookie in: lib/galaxy/web/framework/__init__.py *def set_cookie( self, value, name='galaxysession', path='/',

Re: [galaxy-dev] [galaxy-iuc] Script to help maintain toolshed repos across toolsheds

2013-05-06 Thread Peter Cock
On Thu, May 2, 2013 at 10:24 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, May 2, 2013 at 7:16 AM, Ira Cooke iraco...@gmail.com wrote: Hi all, I've written a script to help deal with the problem of maintaining toolshed tools across multiple toolsheds (eg test and release) The

Re: [galaxy-dev] user password different type encoding

2013-05-06 Thread Vipin TS
Thanks James! I have pulled the recent changes to my repository and this is working fine. I have tested with creating a new user and I tried to login with the recently created user and this works fine at my end. The entry looks like as follows: galaxy=# select username,email,password from

[galaxy-dev] Published Workflows missing from All Workflows

2013-05-06 Thread Peter Cock
Hello all, This is to report a usability bug with workflows - specifically the curiously separate handling of Published Workflows in the user interface. 1. Log into your Galaxy account, 2. On the top ribbon, click on Shared Data, Published Workflows, and make a note of the entries. 3. Return to

[galaxy-dev] List of genomes

2013-05-06 Thread Lee Katz
Hi, I am wondering what I can do to add more genomes to this list (hopefully this image will make it through the mailing list). I am importing fastq files from a MiSeq run. We are using a modified version of Galaxy called Tron. Everything I see on the wiki is about adding custom reference

Re: [galaxy-dev] LWR runner configuration for shared folder in cluster

2013-05-06 Thread John Chilton
On Mon, May 6, 2013 at 9:35 AM, Krampis, Konstantinos kkram...@jcvi.org wrote: Hi John, thanks for the quick reply! It is actually a virtual cluster using virtual machines with VirtualBox, which are brought up via Vagrant (www.vagrantup.com) - that also sets up the shared filesystem. I

Re: [galaxy-dev] LWR runner configuration for shared folder in cluster

2013-05-06 Thread John Chilton
Opps that last message got sent before I meant to. I meant to finish saying that this file would need to be changed: https://bitbucket.org/galaxy/galaxy-central/src/default/lib/galaxy/jobs/runners/lwr.py#cl-80 queue_job() will likely need to skip everything to do with the FileStager class and

Re: [galaxy-dev] Conditional tool options based on input file format?

2013-05-06 Thread Peter Cock
On Fri, Mar 15, 2013 at 2:50 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Peter, I've looked over the wiki and as far as I can see, 'when' tags used inside 'conditional' tags only work on another input variable's values. I would like to be able to do is a

[galaxy-dev] Tophat problem

2013-05-06 Thread Zain A Alvi
Dear Sir or Madam, I hope this reaches you well. Lately, I have been trying to use tophat and then use bowtie on Galaxy project to create an aligned BAM file. The original data came from a SRA file that I have acquired from the Japanese DNA Databank. This SRA was then converted to FASTQ using

Re: [galaxy-dev] Taxonomy fetching not working

2013-05-06 Thread Adam Brenner
Deeps, It does not appear that you have installed taxBuilder on your system. What commands did you use to compile it on your system? If you type 'which taxBuilder' it should return no results (assuming installed incorrectly). You will need to 'make clean' then 'make all' then manually move the

[galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

2013-05-06 Thread Iry Witham
Hi Team, I urgently need to resize the data partition on my galaxy cloudman instance without loosing anything. I notice that there a gui on the cloudman admin page that will allow me to increase it to 1000GB. If I use that will it restart all of the processes? I need to maintain this as a

Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

2013-05-06 Thread Dannon Baker
Hi Iry, This should work, I use it regularly. Just make sure you're not ssh'ed in and 'in' /mnt/galaxyData or anything like that. There's not really another way to do this that I'd recommend trying if you need the instance to continue working for something tomorrow. Let me know if you have any

Re: [galaxy-dev] Published Workflows missing from All Workflows

2013-05-06 Thread Jeremy Goecks
i.e. Published Workflows are hidden or separated away from the others. This appears to be a design choice (like shared datasets they must be imported before use), but if so this could be clarified as follows: This was a very old design choice that will be revisited in the (hopefully near)

Re: [galaxy-dev] Tool Shed Request - sanity check uploads?

2013-05-06 Thread Peter Cock
On Mon, May 6, 2013 at 9:55 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On May 2, 2013, at 12:54 PM, Peter Cock wrote: Another even simpler change (which would also make a big difference) is to actually have the name of the current repository on the Upload a single file or a tarball page.

Re: [galaxy-dev] Published Workflows missing from All Workflows

2013-05-06 Thread Peter Cock
On Mon, May 6, 2013 at 7:08 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote: i.e. Published Workflows are hidden or separated away from the others. This appears to be a design choice (like shared datasets they must be imported before use), but if so this could be clarified as follows: This

[galaxy-dev] Improving the change revision view on the Tool Shed

2013-05-06 Thread Peter Cock
Hello all, I've noticed a couple of weaknesses in the current revision view for the Tool Shed. First, the commit comment is not shown - this would make sense next to the revision number and above the diffs. Second, there is no easy way to jump to the next/prev revision, you must first go back

Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

2013-05-06 Thread Iry Witham
Hi Dannon, I will give it a shot. Are you familiar with the load balancer and how to make it work? Or the auto scaling feature? Thanks, Iry From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com Date: Monday, May 6, 2013 2:06 PM To: Iry Witham

[galaxy-dev] Usability bug/inconsistency with workflows versus tools

2013-05-06 Thread Peter Cock
I seem to be in feedback mode: another little rough edge in Galaxy: When using a tool in Galaxy, at the end of the parameters there is a nice eye catching blue button labelled execute. When running a workflow in Galaxy, the equivalent button is plain grey and reads Run workflow. I think it would

[galaxy-dev] Embedding a help text in a Workflow?

2013-05-06 Thread Peter Cock
Hello all, I've recently started sharing some sample workflows on the Galaxy Tool Shed, http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow When writing a Galaxy tool we have a lot of flexibility within the help tag

Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

2013-05-06 Thread Iry Witham
Hi Dannon, I have attempted the resizing. I clicked on the disk and set it for 1000GB. The instance restarted, but the volume remains at 100GB. Is this due to the lack of disk space? I don't see a snapshot when I look at the AWS console after the restart. Any ideas? Thanks, IRy From:

Re: [galaxy-dev] Usability bug/inconsistency with workflows versus tools

2013-05-06 Thread Dannon Baker
Thanks for the suggestion -- this style should definitely be applied in both places and I've done so in 9659:bcb6e71eda61. -Dannon On Mon, May 6, 2013 at 2:30 PM, Peter Cock p.j.a.c...@googlemail.comwrote: I seem to be in feedback mode: another little rough edge in Galaxy: When using a tool

Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

2013-05-06 Thread Dannon Baker
So you have a cluster with 9 instances and you're using ec2 load balancer with all of them to divert traffic? On Mon, May 6, 2013 at 3:56 PM, Iry Witham iry.wit...@jax.org wrote: I have setup a load balancer, but it shows that only 1 of 9 instances are 'In Service. I have set the health

Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

2013-05-06 Thread Iry Witham
I was not clear how the load balancer worked in this instance, but my goal was to improve performance. I am not sure this was the correct use, but it seemed to work. From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com Date: Monday, May 6, 2013 4:12 PM To: Iry Witham

Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

2013-05-06 Thread Dannon Baker
Ahh, ok. So, unfortunately Cloudman isn't designed to be used with a load balancer (at least at this point). In any given cluster you have exactly one master node and all of the rest are workers (which do not run web processes, hence the 1/9 health). What was slow that you were trying to

Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

2013-05-06 Thread Iry Witham
I did add nodes about the same time I setup load balancing so that was likely the fix. I will definitely set the head node not to run jobs. Thanks, Iry From: Dannon Baker dannon.ba...@gmail.commailto:dannon.ba...@gmail.com Date: Monday, May 6, 2013 4:19 PM To: Iry Witham

Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

2013-05-06 Thread Dannon Baker
Ok, cool. It's worth noting that worker nodes are completely disposable and that if there are any not running jobs at the top of the hour (when billing happens) it's a waste. What you may want to do, at least until the event tomorrow, is scale back down to 1 master and 1 worker node and turn on

Re: [galaxy-dev] user password different type encoding

2013-05-06 Thread Bob Harris
I thought this would be transparent to the users instead of forcing to reset the password. Two thoughts... but please consider that I might not know what I am talking about, and that these might not be good ideas ... (1) James' implementation supports two hashing schemes in the table.

Re: [galaxy-dev] [galaxy-iuc] Script to help maintain toolshed repos across toolsheds

2013-05-06 Thread Greg Von Kuster
Helo Peter and Ira, These are great ideas and contributions, and I'll make sure to incorporate some version of them into the Tool Shed framework as soon as possible. I've created the following Trello card for this. Thanks!

Re: [galaxy-dev] Improving the change revision view on the Tool Shed

2013-05-06 Thread Greg Von Kuster
Hi Peter, Thanks for your message - these should't take long once I'm back to typing with 2 hands. I've added the following Trello card for this. https://trello.com/card/toolshed-page-improvements-and-fixes/506338ce32ae458f6d15e4b3/839 Greg On May 6, 2013, at 2:17 PM, Peter Cock wrote:

Re: [galaxy-dev] List of genomes

2013-05-06 Thread Jeremy Goecks
You can add genomes in this file: $GALAXYROOT/tool-data/shared/ucsc/builds.txt Note that without related files (e.g. genome sequence, indices for mapping), the build information isn't very useful. However, with an entry in this file, you can link it to other resources when they become