Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-28 Thread Greg Von Kuster
Hi lance, Another best practice I should have mentioned: if you are using your TOOL_DEV_LOCAL_DIR as a source code repository for developing your tools (where you are committing tool development change sets into your hg repository in TOOL_DEV_LOCAL_DIR), you should not push the change log

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-27 Thread Lance Parsons
I'm actually still a bit confused as to what the expected workflow is. Should I be able to clone the tool shed repo to my local development workstation (TOOL_DEV_LOCAL_DIR), commit a change, and then push that change back to the Tool Shed? I've added some comments inline to clarify. Greg

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-27 Thread Greg Von Kuster
Hi Lance, On Sep 27, 2012, at 4:37 PM, Lance Parsons wrote: I'm actually still a bit confused as to what the expected workflow is. Should I be able to clone the tool shed repo to my local development workstation (TOOL_DEV_LOCAL_DIR), commit a change, and then push that change back to the

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-25 Thread Lance Parsons
I'm sorry I wasn't more clear. I do believe that those links explain the behavior I am seeing. However, let me try to describe it a different way. It seems that there will, at most, be one installable revision of a given version of a tool. Here I use revision to denote a mercurial revision

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-25 Thread Greg Von Kuster
Hi Lance, I need to figure out precisely what steps you are taking to produce this behavior, as I have not been able to do so. Please see my inline comments, and let me know more information about each step you are taking to produce this behavior. On Sep 25, 2012, at 10:24 AM, Lance Parsons

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-24 Thread Greg Von Kuster
Hi Lance, On Sep 21, 2012, at 6:04 PM, Lance Parsons wrote: OK, I was able to get a new version installed. It seems there are two issues: 1) New revisions with the same version ionvalidate previous revisions. This means that Galaxy servers with the old, and now invalid, revisions are

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-21 Thread Lance Parsons
I've run into this issue again, and I'm having a hard time working around it. However, I have confirmed that at least some updates to a tool in the tool shed will invalidate previously valid revisions and thus prevent users from installing or updating the tool at all. For example, push

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-21 Thread Lance Parsons
OK, I was able to get a new version installed. It seems there are two issues: 1) New revisions with the same version ionvalidate previous revisions. This means that Galaxy servers with the old, and now invalid, revisions are not able to update the tool (nor install it again). 2) Pushes

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-18 Thread Greg Von Kuster
Hello Lance, I've just committed a fix for getting updates to installed tool shed repositories in change set 7713:23107188eab8, which is currently available only in the Galaxy central repository. However, my fix will probably not correct the issue you're describing, and I'm still not able to

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-13 Thread Lance Parsons
Actually, I think that is exactly the issue. I DO have 3:f7a5b54a8d4f installed. I've run into a related issue before, but didn't fully understand it. I believe what happened was: 1) I pushed revision 3:f7a5b54a8d4f to the tool shed which contained the first revision of version 0.2 of the

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-12 Thread Lance Parsons
I've updated my development system now, and when I try to get updates for that particular tool (htseq_count) I run into the following error. Any ideas on how I can/should fix this? Thanks. URL:

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-12 Thread Greg Von Kuster
Hi Lance, What is the changeset revision that you installed? It looks like you could only have installed one of the following 3 revisions: 1:14e18dc9ed13 2:f5d08224af89 4:14bec14f4290 Since you could not have installed 3:f7a5b54a8d4f, I'm not quite sure how you could be trying to update to

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-11 Thread Lance Parsons
Thanks Greg. I used you're updated version and added numpy as a separate dependency. It seems to work in my development system. I haven't updated my qa or production versions yet, so I can't check there. Perhaps you could test it and let me know if there are issues, etc. Glad I can be of

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-07 Thread Greg Von Kuster
Hello Lance, See my inline comments. On Sep 4, 2012, at 3:15 PM, Lance Parsons wrote: I've put together a tool wrapper for the htseq-count script that is part of the HTSeq python package and uploaded that to the tool shed. However, I have discovered that the tool dependancies do not

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-04 Thread Greg Von Kuster
Hi Lance, Thanks for reporting these issues - the tool dependencies component is fairly new, so you may have uncovered some problems that need correction. I'll take a look at these. make corrections if necessary, and get back to you when all is functional. Thanks! Greg Von Kuster On Sep 4,