Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-11-18 Thread Peter Cock
On Thu, Nov 14, 2013 at 4:35 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Dave, Good news, the BLAST+ tests appear to have all passed on the Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/f2478dc77ccb ... Over on the main Tool Shed, the binary

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-11-14 Thread Peter Cock
On Tue, Nov 12, 2013 at 3:33 AM, Dave Bouvier d...@bx.psu.edu wrote: Peter, Thanks for bringing this to our attention, we're working on fixing a number of issues with the test framework, and hope to have more information for you tomorrow. --Dave B. Hi Dave, Good news, the BLAST+ tests

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-11-14 Thread Nate Coraor
Bash is easily obtained on these systems and I think the extra functionality available in post-Bourne shells ought to be allowed. I also question how many people are going to run tools on *BSD since most underlying analysis tools tend to only target Linux. That said, shell code should be

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-11-14 Thread Peter Cock
On Thu, Nov 14, 2013 at 5:13 PM, Nate Coraor n...@bx.psu.edu wrote: Bash is easily obtained on these systems and I think the extra functionality available in post-Bourne shells ought to be allowed. I also question how many people are going to run tools on *BSD since most underlying analysis

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-11-14 Thread Nate Coraor
On Nov 14, 2013, at 12:21 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Nov 14, 2013 at 5:13 PM, Nate Coraor n...@bx.psu.edu wrote: Bash is easily obtained on these systems and I think the extra functionality available in post-Bourne shells ought to be allowed. I also question how

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-11-14 Thread Greg Von Kuster
If, by current installation methods you are not referring to Tool Shed repository installation methods for installing tool dependencies, then please read no further. For installing tool dependencies along with repositories from the Tool Shed, fabric is currently being used. However, it's been

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-11-11 Thread Peter Cock
Hi Dave, I think this is a new regression from the Test Tool Shed installation framework, http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/f2478dc77ccb Tool test results Automated test environment Tools missing tests or test data Installation errors - no functional tests were run

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-11-11 Thread James Taylor
This is not an objection, but do we need bash? Can we live with posix sh? We should ask this question about every requirement we introduce. (bash is not part of the default installation of FreeBSD or OpenBSD for example. bash is unfortunately licensed under GPLV3, so if you are trying to create

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-11-11 Thread Dave Bouvier
Peter, Thanks for bringing this to our attention, we're working on fixing a number of issues with the test framework, and hope to have more information for you tomorrow. --Dave B. On 2013-11-11 06:11, Peter Cock wrote: Hi Dave, I think this is a new regression from the Test Tool Shed

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-10-07 Thread Peter Cock
On Tue, Sep 24, 2013 at 10:58 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, Some good news, the strange missing /bin/sh error has gone away on the Test Tool Shed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/aecdffbc08fc The BLAST+ wrapper tests also look good

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-10-07 Thread Dave Bouvier
Peter, I did some investigating, and it turns out that the if [[ condition ]] syntax used in the ncbi tool dependency is only compatible with bash, not sh. For sh, the corresponding syntax would look like: if [ $string = value ] then echo string is equal to value fi However, it strikes

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-10-07 Thread Peter Cock
On Mon, Oct 7, 2013 at 3:37 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I did some investigating, and it turns out that the if [[ condition ]] syntax used in the ncbi tool dependency is only compatible with bash, not sh. Does that mean the test system has switched between sh and bash and

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-10-07 Thread Peter Cock
On Mon, Oct 7, 2013 at 3:44 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Oct 7, 2013 at 3:37 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I did some investigating, and it turns out that the if [[ condition ]] syntax used in the ncbi tool dependency is only compatible with bash,

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-10-07 Thread Dave Bouvier
Peter, The platform detection code is not yet in the stable branch, but is intended to be included in the upcoming release. The automated testing framework does run the default branch, though, so the nightly tests will make use of the new definitions. --Dave B. On 10/07/2013 11:22 AM,

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-10-07 Thread Nicola Soranzo
actions_group is neither in stable nor in default branch of galaxy-dist repository, it's present only in galaxy-central. Nicola Il giorno lun, 07/10/2013 alle 11.24 -0400, Dave Bouvier ha scritto: Peter, The platform detection code is not yet in the stable branch, but is intended to be

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-10-07 Thread John Chilton
On Mon, Oct 7, 2013 at 10:22 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Oct 7, 2013 at 3:44 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Oct 7, 2013 at 3:37 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I did some investigating, and it turns out that the if [[

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-10-07 Thread Peter Cock
On Mon, Oct 7, 2013 at 4:45 PM, Nicola Soranzo sora...@crs4.it wrote: actions_group is neither in stable nor in default branch of galaxy-dist repository, it's present only in galaxy-central. Nicola i.e. for now only they can only be used and tested on the Test Tool Shed? It would be helpful

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-10-07 Thread Björn Grüning
Am Montag, den 07.10.2013, 10:36 -0500 schrieb John Chilton: On Mon, Oct 7, 2013 at 10:22 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Oct 7, 2013 at 3:44 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Oct 7, 2013 at 3:37 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter,

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-09-24 Thread Peter Cock
Hi all, Some good news, the strange missing /bin/sh error has gone away on the Test Tool Shed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/aecdffbc08fc The BLAST+ wrapper tests also look good on the main Tool Shed: http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-09-23 Thread Peter Cock
On Fri, Sep 20, 2013 at 11:10 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Sep 18, 2013 at 11:47 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Aug 27, 2013 at 2:18 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I also tried running the command that returns error code 64

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-09-20 Thread Peter Cock
On Wed, Sep 18, 2013 at 11:47 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Aug 27, 2013 at 2:18 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I also tried running the command that returns error code 64 on the same system that runs the automated tests, and it downloaded the correct

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-09-18 Thread Peter Cock
On Tue, Aug 27, 2013 at 2:18 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I also tried running the command that returns error code 64 on the same system that runs the automated tests, and it downloaded the correct file for that operating system and architecture. So I'm not sure why it's

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-09-01 Thread Guest, Simon
Simon wrote: An example is the NCBI BLAST+ suite, which failed to build on my (EL6) system, because it couldn't run /usr/bin/touch. That's pretty dumb, and pretty simple to solve in isolation - it needs to be running /bin/touch instead. This was an oddity in the NCBI compile scripts

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-08-30 Thread Peter Cock
Hi Simon, Further to our discussion here: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016310.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016316.html Simon wrote: An example is the NCBI BLAST+ suite, which failed to build on my (EL6) system, because it couldn't

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-08-27 Thread Dave Bouvier
Peter, I also tried running the command that returns error code 64 on the same system that runs the automated tests, and it downloaded the correct file for that operating system and architecture. So I'm not sure why it's failing when run through buildbot, but I'll look into it and get back to

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-08-26 Thread Dave Bouvier
Peter, I apologize for the delay, here is the information you requested: ubuntu@ip-10-0-0-243:~$ uname -a Linux ip-10-0-0-243 3.8.0-25-generic #37-Ubuntu SMP Thu Jun 6 20:47:07 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux ubuntu@ip-10-0-0-243:~$ arch x86_64 ubuntu@ip-10-0-0-243:~$ echo $0 -bash

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-08-26 Thread Peter Cock
On Mon, Aug 26, 2013 at 3:10 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I apologize for the delay, here is the information you requested: ubuntu@ip-10-0-0-243:~$ uname -a Linux ip-10-0-0-243 3.8.0-25-generic #37-Ubuntu SMP Thu Jun 6 20:47:07 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-08-26 Thread Björn Grüning
Hi Dave, I can confirm that it is also working for me. uname -a Linux threonin 3.5.0-36-generic #57-Ubuntu SMP Wed Jun 19 15:10:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux bag@threonin:~/projects/github/galaxytools$ arch x86_64 bag@threonin:~/projects/github/galaxytools$ echo $0 bash Is the

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-08-21 Thread Peter Cock
On Tue, Aug 20, 2013 at 9:15 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I believe this was again due to the installation of an earlier repository hanging until the testing framework canceled the build. I've added the repository in question to the exclude list, and hopefully your blast

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-08-21 Thread Peter Cock
On Wed, Aug 21, 2013 at 10:54 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Aug 20, 2013 at 9:15 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I believe this was again due to the installation of an earlier repository hanging until the testing framework canceled the build. I've

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-08-21 Thread Dave Bouvier
Peter, Here is the relevant log output for the installation of ncbi_blast_plus. A quick google informs me that exit code 64 means command line usage error, for what it's worth. install_and_test_repositories INFO 2013-08-20 23:34:43,270 Installing and testing revision 946749c8605f of

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-08-21 Thread Peter Cock
On Wed, Aug 21, 2013 at 1:45 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, Here is the relevant log output for the installation of ncbi_blast_plus. A quick google informs me that exit code 64 means command line usage error, for what it's worth. install_and_test_repositories INFO 2013-08-20

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-08-16 Thread Peter Cock
On Wed, Aug 14, 2013 at 2:25 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Aug 14, 2013 at 11:56 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Greg, I'm hoping you (or Dave) can throw a little light on why the NCBI BLAST+ nightly tests are not working again yet: ... Sadly

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-08-14 Thread Peter Cock
Hi Greg, I'm hoping you (or Dave) can throw a little light on why the NCBI BLAST+ nightly tests are not working again yet: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/949fa0294c0d e.g. Fatal error: Exit code 127 () /bin/sh: 1: blastn: not found /bin/sh: 1: blastn: not found

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-08-14 Thread Peter Cock
On Wed, Aug 14, 2013 at 11:56 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Greg, I'm hoping you (or Dave) can throw a little light on why the NCBI BLAST+ nightly tests are not working again yet: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/949fa0294c0d e.g. Fatal

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-08-07 Thread Peter Cock
On Wed, Aug 7, 2013 at 3:36 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, On Aug 7, 2013, at 10:26 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Greg et al, For the NCBI BLAST+ wrappers, Nicola has suggested we split out the binaries themselves into a separate Tool Shed

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-08-07 Thread Peter Cock
On Wed, Aug 7, 2013 at 3:54 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Aug 7, 2013 at 3:36 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, On Aug 7, 2013, at 10:26 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Greg et al, For the NCBI BLAST+ wrappers, Nicola has

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-08-07 Thread Bjoern Gruening
Hi Peter, On Wed, Aug 7, 2013 at 3:54 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Aug 7, 2013 at 3:36 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, On Aug 7, 2013, at 10:26 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Greg et al, For the NCBI BLAST+

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-08-07 Thread Peter Cock
On Wed, Aug 7, 2013 at 5:11 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Peter, Now, back in ncbi_blast_plus, I have revised the repository_dependencies.xml to declare this new repository dependency (the revision tag etc is missing to mean the latest version at upload is used):

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

2013-08-07 Thread Peter Cock
On Wed, Aug 7, 2013 at 5:35 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Aug 7, 2013 at 5:11 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Peter, Now, back in ncbi_blast_plus, I have revised the repository_dependencies.xml to declare this new repository dependency (the