Re: [galaxy-dev] Tools to download SRA datasets from GEO

[Ryan G]

Thanks Hans-Rudolf.  I didn't see the EBI SRA link before.  But not sure
what will do what I want.  I want to be able to plug in an SRA # and have
the tool download the data and prep it for analysis.  Right now, it looks
like I need to click through the EBI website to get the data.  I found a
tool in the toolshed but haven't had a chance to look at it. That is my
next step.

On Thu, Feb 5, 2015 at 3:18 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:

 Hi

 Are you looking for any special GEO data, which is not mirrored at the
 ENA? If not, you can probaly use the  Get Data - EBI SRA tool, which
 is part of the installation.

 Also, have you looked at the toolshed? e.g.
 https://toolshed.g2.bx.psu.edu/view/matt-shirley/ncbi_sra_toolkit


 Regards, Hans-Rudolf



 On 02/04/2015 04:44 PM, Ryan G wrote:

 Do any tools exist to download GEO datasets from NCBI?




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[galaxy-dev] Manually adding new tools from toolshed

[Ryan G]

Because of the way the infrastructure for my Galaxy instance is set up, I
need to download and install tools from the toolshed manually.  For most of
the tools, this is pretty easy, however I'm now trying to add RSEM to my
instance and it has some new datatypes.

Along with the new data types is python class file.  I'm referring to the
exist datatypes_conf.xml.sample but don't see a reference to datatype_files
as is coded in the RSEM tool.

So my question is, how can I manually install a tool such as RSEM from the
toolshed?  I've cloned it but not sure where to put the files and what to
modify in Galaxy's configuration to see the new files.  I can modify the
datatypes_conf.xml and include the datatypes, but I get the sense this is
not correct.

Ryan
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[galaxy-dev] Manually installing rsem_datatypes package from toolshed

[Ryan G]

I'm trying to manually install rsem_datatypes package into my local Galaxy
install.  I can't use the Toolshed for various reasons.

Anyway, I downloaded the package using

hg clone https://toolshed.g2.bx.psu.edu/repos/jjohnson/rsem_datatypes

I see two files:

1)  datatypes_conf.xml, and
2) rsem.py

I copied the datatype extension ... lines into my
config/datatypes_conf.xml file.
I also copied  rsem.py to lib/galaxy/datatypes/.

When I restart Galaxy, it doesn't seem that Galaxy knows how to handle rsem
datatypes, as I get this error:

galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,519 Error importing
datatype module galaxy.datatypes.rsem: 'module' object has no attribute
'rsem'
Traceback (most recent call last):
  File /data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py, line
210, in load_datatypes
module = getattr( module, mod )
AttributeError: 'module' object has no attribute 'rsem'
galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,519 Error importing
datatype module galaxy.datatypes.rsem: 'module' object has no attribute
'rsem'
Traceback (most recent call last):
  File /data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py, line
210, in load_datatypes
module = getattr( module, mod )
AttributeError: 'module' object has no attribute 'rsem'
galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,520 Error importing
datatype module galaxy.datatypes.rsem: 'module' object has no attribute
'rsem'
Traceback (most recent call last):
  File /data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py, line
210, in load_datatypes
module = getattr( module, mod )
AttributeError: 'module' object has no attribute 'rsem'

I'm obviously missing something but not sure what.  I suspect maybe the
rsem.py file is not in the right place?

Ryan
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Re: [galaxy-dev] Manually adding new tools from toolshed

[Ryan G]

I can try a local toolshed, but the organization I work at frowns upon
automatic installation for various reasons.  That and it lets me see
exactly how a tool is installed and works within my local instance.

When a tool is installed from the toolshed, how does Galaxy know about it?
From a DB entry, or from the XML file(s) being present somewhere?  I sort
of like the idea of how /etc/profile.d gets scanned by /etc/bashrc when a
user logs into a linux machine.  This way, there is no modification of
files, just placing the right files in the right directory is all that is
needed.  Anyway, I need to understand how Galaxy works with the toolshed.

On Fri, Jan 16, 2015 at 3:08 AM, Björn Grüning bjoern.gruen...@gmail.com
wrote:

 Hi Ryan,

 what about a local bootstrapped ToolShed which is in sync with the
 public one (at least for the users you are interested on). Than you can
 install from this ToolShed. I guess this is less annoying than
 maintaining everything on your own.

 Cheers,
 Bjoern

 Am 16.01.2015 um 08:22 schrieb Peter Cock:
  On Thu, Jan 15, 2015 at 6:57 PM, Ryan G ngsbioinformat...@gmail.com
 wrote:
  Because of the way the infrastructure for my Galaxy instance is set up,
 I
  need to download and install tools from the toolshed manually.  For
 most of
  the tools, this is pretty easy, however I'm now trying to add RSEM to my
  instance and it has some new datatypes.
 
  Along with the new data types is python class file.  I'm referring to
 the
  exist datatypes_conf.xml.sample but don't see a reference to
 datatype_files
  as is coded in the RSEM tool.
 
  So my question is, how can I manually install a tool such as RSEM from
 the
  toolshed?  I've cloned it but not sure where to put the files and what
 to
  modify in Galaxy's configuration to see the new files.  I can modify the
  datatypes_conf.xml and include the datatypes, but I get the sense this
 is
  not correct.
 
  Ryan
 
  The old pre-ToolShed way to add a new datatype was indeed to
  add it to datatypes_conf.xml and put any Python file into the
  galaxy-dist/lib/galaxy/datatypes/
 
  I'm still doing this on some of my locally developed tools, but
  now they are in the ToolShed perhaps I should switch to using
  that...
 
  Regards,
 
  Peter
 
  P.S. You also used to need to add an import line to the
  galaxy-dist/lib/galaxy/datatypes/registry.py but that is not
  longer required as of this bug fix:
 
 https://bitbucket.org/galaxy/galaxy-central/commits/1422966f1ca88472b8685015f5a8cdd3dd0f1db9
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Re: [galaxy-dev] Manually installing rsem_datatypes package from toolshed

[Ryan G]

Yup, that fixed it. Thanks!

On Wed, Jan 21, 2015 at 6:51 PM, John Chilton jmchil...@gmail.com wrote:

 I believe this is an ancient bug that I has been fixed in Galaxy's
 central branch but is not in the latest release:


 https://bitbucket.org/galaxy/galaxy-central/commits/1422966f1ca88472b8685015f5a8cdd3dd0f1db9

 The previous workaround for this bug was that one would need to import
 the datatype at the top of registry.py (import rsem_datatypes) which
 is another option for addressing this problem instead of applying the
 patch.

 Hope this helps,
 -John


 On Wed, Jan 21, 2015 at 2:16 PM, Ryan G ngsbioinformat...@gmail.com
 wrote:
  I'm trying to manually install rsem_datatypes package into my local
 Galaxy
  install.  I can't use the Toolshed for various reasons.
 
  Anyway, I downloaded the package using
 
  hg clone https://toolshed.g2.bx.psu.edu/repos/jjohnson/rsem_datatypes
 
  I see two files:
 
  1)  datatypes_conf.xml, and
  2) rsem.py
 
  I copied the datatype extension ... lines into my
  config/datatypes_conf.xml file.
  I also copied  rsem.py to lib/galaxy/datatypes/.
 
  When I restart Galaxy, it doesn't seem that Galaxy knows how to handle
 rsem
  datatypes, as I get this error:
 
  galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,519 Error importing
  datatype module galaxy.datatypes.rsem: 'module' object has no attribute
  'rsem'
  Traceback (most recent call last):
File /data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py, line
  210, in load_datatypes
  module = getattr( module, mod )
  AttributeError: 'module' object has no attribute 'rsem'
  galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,519 Error importing
  datatype module galaxy.datatypes.rsem: 'module' object has no attribute
  'rsem'
  Traceback (most recent call last):
File /data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py, line
  210, in load_datatypes
  module = getattr( module, mod )
  AttributeError: 'module' object has no attribute 'rsem'
  galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,520 Error importing
  datatype module galaxy.datatypes.rsem: 'module' object has no attribute
  'rsem'
  Traceback (most recent call last):
File /data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py, line
  210, in load_datatypes
  module = getattr( module, mod )
  AttributeError: 'module' object has no attribute 'rsem'
 
  I'm obviously missing something but not sure what.  I suspect maybe the
  rsem.py file is not in the right place?
 
  Ryan
 
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Re: [galaxy-dev] Problem using FastQC in Galaxy

[Ryan G]

I hate to hijack this thread, but I was thinking about this over the
holiday in how we are going to maintain a local up to date copy of Galaxy
ourselves.  One thought would be to standardize on a single supported
platform aka an Amazon instance and make sure everything works on that
single platform.  This frees you from having to support many different
platforms and versions.  Have you guys given this some thought?

On Mon, Jan 5, 2015 at 12:05 PM, Nate Coraor n...@bx.psu.edu wrote:

 Hi Michael,

 I understand your frustration in this regard. We do make an effort to
 respond to and fix issues that people encounter when upgrading Galaxy
 releases. We've also made pretty significant strides in increasing the
 quality of our releases, including a feature freeze for at least 2 weeks
 prior to each release. The galaxy-dev mailing list is fairly active, as is
 our IRC channel (#galaxyproject on Freenode) for more real-time help.

 If you're not familiar with the Galaxy News Briefs, these are the primary
 means of communicating the changes you should expect to see between Galaxy
 releases and any config changes that might be necessary between releases:

 https://wiki.galaxyproject.org/DevNewsBriefs

 We also recommend having a Test/QA Galaxy server (or cloning your
 production Galaxy instance) to test an upgrade before deploying it on your
 production instance(s) so most problems can be caught beforehand.

 Unfortunately, due to the wide range of platforms, deployment scenarios,
 site-specific factors, and large scope of Galaxy functionality, we can't
 catch all potential issues. I don't think this is outside the rate
 typically experienced with major releases of large open source software,
 but it is still frustrating when it occurs. That said, we'll do our best to
 assist and improve documentation when you do encounter upgrade problems.

 --nate


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Re: [galaxy-dev] Mercurial is out of date for Toolshed

[Ryan G]

Thanks.  Is there an alternative way I can install tools from the
Toolshed?  This problem pretty much renders the toolshed unusable for me...

On Mon, Jan 5, 2015 at 11:14 AM, John Chilton jmchil...@gmail.com wrote:

 It is certainly the case that Galaxy should be using the latest
 version of mercurial given a number of high profile bugs with older
 versions. Unfortunately it doesn't seem possible to just drop the new
 version it - there are some API changes that prevent Galaxy from
 loading when doing this and the number of people who can add new eggs
 to Galaxy is low.

 I have created a Trello card to track this issue:

 https://trello.com/c/9A9uIav0

 Let us know if you happen to find a workaround for this issue.

 -John


 On Mon, Dec 22, 2014 at 2:55 PM, Ryan G ngsbioinformat...@gmail.com
 wrote:
  I've been trying to track down why I can't get anything from the toolshed
  installed and finally have it figured out.
 
  Whenever I tried to install anything I always got an Error with no
  explanation of what the error was.  After enabling Debug messages into
 the
  log file, I see the error is:
 
  tool_shed.util.hg_util DEBUG 2014-12-22 14:47:48,910 Error cloning
  repository: httpsconnection instance has no attribute '_set_hostport'
 
  I googled around and found out this is a known bug/issue with older
 version
  of Mercurial and was fixed in v3.
 
  I added a line to hg_util.py to see where it picks up hg.  Its using
 version
  2.2.3.  Indeed, one of the eggs downloaded by Galaxy is mercurial-2.2.3.
 
  I have the newest version of mercurial installed in my site-packages
 folder
  but I guess that's not what galaxy wants.  So my question is, how do I
 get
  Galaxy to use the latest version of Mercurial?  And, Why did it download
 an
  older version?
 
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[galaxy-dev] FastQC wrapper not seeing files at gzipped

[Ryan G]

Hi all - I've got a bunch of fatsq files uploaded into a data library in
Galaxy.  The underlying files is gzipped however Galaxy strips the .gz from
the filename and displays it as .fastq.  When the python wrapper
rgFastQC.py gets called, it correctly sees the fastq.gz file.  The wrapper
creates a symbolic link to the .gz file in a tmp directory.  The link is
.fastq.  When FastQC tries to read this file, it fails because its
compressed.  So one of two things is going wrong here:

1)  It looks like the wrapper is incorrectly renaming the file, but its
using the name given to it in Galaxy.

2)  When the file is uploaded into the data library, Galaxy is stripping
off the .gz extension.

I think #2 is the more correct problem.  How can I keep Galaxy from
stripping the .gz extension?
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Re: [galaxy-dev] FastQC wrapper not seeing files at gzipped

[Ryan G]

To (I think) fix this, I changed line 50 in rgFastQC.py from
infname = self.opts.inputfilename

to
infname = self.opts.input

This will force FastQC to look at the real file and not the renamed
dataset.


On Mon, Jan 12, 2015 at 12:20 PM, Ryan G ngsbioinformat...@gmail.com
wrote:

 Yes, I'm doing a link to file on file system when doing a library import.
 Does this mean I should link to the the uncompressed file?

 On Mon, Jan 12, 2015 at 12:14 PM, Peter Cock p.j.a.c...@googlemail.com
 wrote:

 Ah. Then this is more subtle... are you using the
 library import option where Galaxy just symlinks
 to existing files? I thought that was not possible
 with gzipped files (for the reasons given below).
 Perhaps this is not being blocked, leading to the
 confused state you're seeing?

 Peter

 On Mon, Jan 12, 2015 at 4:52 PM, Ryan G ngsbioinformat...@gmail.com
 wrote:
  Galaxy is not decompressing the file.  The file is linked to on the
  filesystem.
 
  On Mon, Jan 12, 2015 at 10:28 AM, Peter Cock p.j.a.c...@googlemail.com
 
  wrote:
 
  Hi Ryan,
 
  The problem isn't Galaxy stripping the extension, rather
  Galaxy is actually decompressing the file as part of the
  upload process.
 
  Unfortunately (and there is an open Trello enhancement
  request on this), Galaxy does not support sorting any of
  the defined datatypes in compressed form UNLESS they
  are defined that way (like BAM files).
 
  This has lead some Galaxy Admins to define a new datatype
  lgzippedfastq (or similar - I'd have to check my old emails
  for the exact name used as a gripped alternative to the
  Galaxy sangerfastq datatype) and then modified many/all
  their tools to handle this. That is a lot of work, but does
  offer big disk savings for this key datatype.
 
  The Galaxy team instead use a compressed file system,
  so for usegalaxy.org ALL their data files are compressed
  but Galaxy can ignore this complexity.
 
  Peter
 
  On Mon, Jan 12, 2015 at 3:15 PM, Ryan G ngsbioinformat...@gmail.com
  wrote:
   Hi all - I've got a bunch of fatsq files uploaded into a data
 library in
   Galaxy.  The underlying files is gzipped however Galaxy strips the
 .gz
   from
   the filename and displays it as .fastq.  When the python wrapper
   rgFastQC.py
   gets called, it correctly sees the fastq.gz file.  The wrapper
 creates a
   symbolic link to the .gz file in a tmp directory.  The link is
 .fastq.
   When
   FastQC tries to read this file, it fails because its compressed.  So
 one
   of
   two things is going wrong here:
  
   1)  It looks like the wrapper is incorrectly renaming the file, but
 its
   using the name given to it in Galaxy.
  
   2)  When the file is uploaded into the data library, Galaxy is
 stripping
   off
   the .gz extension.
  
   I think #2 is the more correct problem.  How can I keep Galaxy from
   stripping the .gz extension?
  
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Re: [galaxy-dev] FastQC wrapper not seeing files at gzipped

[Ryan G]

Agreed.

On Mon, Jan 12, 2015 at 10:24 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:

 Hi Ryan,

 That is the workaround I am using, which means
 keeping an uncompressed copy of the FASTQ
 file on our main storage from where Galaxy can
 see it (for people to use within their histories).

 From a long term storage perspective this is not
 ideal - so I am keen for better handling of gzipped
 files within Galaxy (particularly within libraries
 which we use for raw data).

 Peter

 On Mon, Jan 12, 2015 at 5:20 PM, Ryan G ngsbioinformat...@gmail.com
 wrote:
  Yes, I'm doing a link to file on file system when doing a library import.
  Does this mean I should link to the the uncompressed file?
 
  On Mon, Jan 12, 2015 at 12:14 PM, Peter Cock p.j.a.c...@googlemail.com
  wrote:
 
  Ah. Then this is more subtle... are you using the
  library import option where Galaxy just symlinks
  to existing files? I thought that was not possible
  with gzipped files (for the reasons given below).
  Perhaps this is not being blocked, leading to the
  confused state you're seeing?
 
  Peter
 
  On Mon, Jan 12, 2015 at 4:52 PM, Ryan G ngsbioinformat...@gmail.com
  wrote:
   Galaxy is not decompressing the file.  The file is linked to on the
   filesystem.
  

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Re: [galaxy-dev] FastQC wrapper not seeing files at gzipped

[Ryan G]

Galaxy is not decompressing the file.  The file is linked to on the
filesystem.

On Mon, Jan 12, 2015 at 10:28 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:

 Hi Ryan,

 The problem isn't Galaxy stripping the extension, rather
 Galaxy is actually decompressing the file as part of the
 upload process.

 Unfortunately (and there is an open Trello enhancement
 request on this), Galaxy does not support sorting any of
 the defined datatypes in compressed form UNLESS they
 are defined that way (like BAM files).

 This has lead some Galaxy Admins to define a new datatype
 lgzippedfastq (or similar - I'd have to check my old emails
 for the exact name used as a gripped alternative to the
 Galaxy sangerfastq datatype) and then modified many/all
 their tools to handle this. That is a lot of work, but does
 offer big disk savings for this key datatype.

 The Galaxy team instead use a compressed file system,
 so for usegalaxy.org ALL their data files are compressed
 but Galaxy can ignore this complexity.

 Peter

 On Mon, Jan 12, 2015 at 3:15 PM, Ryan G ngsbioinformat...@gmail.com
 wrote:
  Hi all - I've got a bunch of fatsq files uploaded into a data library in
  Galaxy.  The underlying files is gzipped however Galaxy strips the .gz
 from
  the filename and displays it as .fastq.  When the python wrapper
 rgFastQC.py
  gets called, it correctly sees the fastq.gz file.  The wrapper creates a
  symbolic link to the .gz file in a tmp directory.  The link is .fastq.
 When
  FastQC tries to read this file, it fails because its compressed.  So one
 of
  two things is going wrong here:
 
  1)  It looks like the wrapper is incorrectly renaming the file, but its
  using the name given to it in Galaxy.
 
  2)  When the file is uploaded into the data library, Galaxy is stripping
 off
  the .gz extension.
 
  I think #2 is the more correct problem.  How can I keep Galaxy from
  stripping the .gz extension?
 
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Re: [galaxy-dev] FastQC wrapper not seeing files at gzipped

[Ryan G]

Yes, I'm doing a link to file on file system when doing a library import.
Does this mean I should link to the the uncompressed file?

On Mon, Jan 12, 2015 at 12:14 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:

 Ah. Then this is more subtle... are you using the
 library import option where Galaxy just symlinks
 to existing files? I thought that was not possible
 with gzipped files (for the reasons given below).
 Perhaps this is not being blocked, leading to the
 confused state you're seeing?

 Peter

 On Mon, Jan 12, 2015 at 4:52 PM, Ryan G ngsbioinformat...@gmail.com
 wrote:
  Galaxy is not decompressing the file.  The file is linked to on the
  filesystem.
 
  On Mon, Jan 12, 2015 at 10:28 AM, Peter Cock p.j.a.c...@googlemail.com
  wrote:
 
  Hi Ryan,
 
  The problem isn't Galaxy stripping the extension, rather
  Galaxy is actually decompressing the file as part of the
  upload process.
 
  Unfortunately (and there is an open Trello enhancement
  request on this), Galaxy does not support sorting any of
  the defined datatypes in compressed form UNLESS they
  are defined that way (like BAM files).
 
  This has lead some Galaxy Admins to define a new datatype
  lgzippedfastq (or similar - I'd have to check my old emails
  for the exact name used as a gripped alternative to the
  Galaxy sangerfastq datatype) and then modified many/all
  their tools to handle this. That is a lot of work, but does
  offer big disk savings for this key datatype.
 
  The Galaxy team instead use a compressed file system,
  so for usegalaxy.org ALL their data files are compressed
  but Galaxy can ignore this complexity.
 
  Peter
 
  On Mon, Jan 12, 2015 at 3:15 PM, Ryan G ngsbioinformat...@gmail.com
  wrote:
   Hi all - I've got a bunch of fatsq files uploaded into a data library
 in
   Galaxy.  The underlying files is gzipped however Galaxy strips the .gz
   from
   the filename and displays it as .fastq.  When the python wrapper
   rgFastQC.py
   gets called, it correctly sees the fastq.gz file.  The wrapper
 creates a
   symbolic link to the .gz file in a tmp directory.  The link is .fastq.
   When
   FastQC tries to read this file, it fails because its compressed.  So
 one
   of
   two things is going wrong here:
  
   1)  It looks like the wrapper is incorrectly renaming the file, but
 its
   using the name given to it in Galaxy.
  
   2)  When the file is uploaded into the data library, Galaxy is
 stripping
   off
   the .gz extension.
  
   I think #2 is the more correct problem.  How can I keep Galaxy from
   stripping the .gz extension?
  
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Re: [galaxy-dev] Mercurial is out of date for Toolshed

[Ryan G]

Yes, I will look at this this week.  I'm using a clean copy of galaxy-dist
and will apply against that to see how it works.  Thanks a bunch Dave B for
doing this!

On Thu, Jan 8, 2015 at 9:42 AM, John Chilton jmchil...@gmail.com wrote:

 Hey Ryan,

 It looks like Dave B. has come to rescue with an egg and a patch that
 implements this:


 https://bitbucket.org/galaxy/galaxy-central/pull-request/626/upgrade-mercurial-egg-to-324

 It probably won't be back-ported to the forthcoming January release
 but I would suspect the raw patch
 (
 https://api.bitbucket.org/2.0/repositories/galaxy/galaxy-central/diff/davebgx/galaxy-central:625bf1fd88ee..63d901ca0e6e
 )
 will apply cleanly against the last few releases. If you have some
 time and want to apply it to your release and let us know if it fixes
 your problems that would probably help the pull request along.

 -John

 On Wed, Jan 7, 2015 at 10:56 AM, Ryan G ngsbioinformat...@gmail.com
 wrote:
  Yes, I think I found the root cause...its because the Galaxy egg for
  mercurial is using an older version of Mercurial that has this known bug.
  The only real fix is to upgrade the Galaxy egg to mercurial 3.x.
 
  The only way I know of to test this is to build a new Galaxy egg which
 I'm
  not familiar with.  But as I understand it the new Mercurial version will
  also break Galaxy.
 
 
  On Mon, Jan 5, 2015 at 6:19 PM, Björn Grüning bjoern.gruen...@gmail.com
 
  wrote:
 
  Hi Ryan,
 
  unfortunately not (yet). But I'm really surprised you are getting this
  error. It working for me and in our docker containers and other
  deployments. Can we try to detect the root cause of this error? Do you
  have conflicting mercurial version.
 
  Cheers,
  Bjoern
 
   Thanks.  Is there an alternative way I can install tools from the
   Toolshed?  This problem pretty much renders the toolshed unusable for
   me...
  
   On Mon, Jan 5, 2015 at 11:14 AM, John Chilton jmchil...@gmail.com
   wrote:
  
   It is certainly the case that Galaxy should be using the latest
   version of mercurial given a number of high profile bugs with older
   versions. Unfortunately it doesn't seem possible to just drop the new
   version it - there are some API changes that prevent Galaxy from
   loading when doing this and the number of people who can add new eggs
   to Galaxy is low.
  
   I have created a Trello card to track this issue:
  
   https://trello.com/c/9A9uIav0
  
   Let us know if you happen to find a workaround for this issue.
  
   -John
  
  
   On Mon, Dec 22, 2014 at 2:55 PM, Ryan G ngsbioinformat...@gmail.com
 
   wrote:
   I've been trying to track down why I can't get anything from the
   toolshed
   installed and finally have it figured out.
  
   Whenever I tried to install anything I always got an Error with no
   explanation of what the error was.  After enabling Debug messages
 into
   the
   log file, I see the error is:
  
   tool_shed.util.hg_util DEBUG 2014-12-22 14:47:48,910 Error cloning
   repository: httpsconnection instance has no attribute
 '_set_hostport'
  
   I googled around and found out this is a known bug/issue with older
   version
   of Mercurial and was fixed in v3.
  
   I added a line to hg_util.py to see where it picks up hg.  Its using
   version
   2.2.3.  Indeed, one of the eggs downloaded by Galaxy is
   mercurial-2.2.3.
  
   I have the newest version of mercurial installed in my site-packages
   folder
   but I guess that's not what galaxy wants.  So my question is, how
 do I
   get
   Galaxy to use the latest version of Mercurial?  And, Why did it
   download
   an
   older version?
  
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Re: [galaxy-dev] Mercurial is out of date for Toolshed

[Ryan G]

Yes, I think I found the root cause...its because the Galaxy egg for
mercurial is using an older version of Mercurial that has this known bug.
The only real fix is to upgrade the Galaxy egg to mercurial 3.x.

The only way I know of to test this is to build a new Galaxy egg which I'm
not familiar with.  But as I understand it the new Mercurial version will
also break Galaxy.


On Mon, Jan 5, 2015 at 6:19 PM, Björn Grüning bjoern.gruen...@gmail.com
wrote:

 Hi Ryan,

 unfortunately not (yet). But I'm really surprised you are getting this
 error. It working for me and in our docker containers and other
 deployments. Can we try to detect the root cause of this error? Do you
 have conflicting mercurial version.

 Cheers,
 Bjoern

  Thanks.  Is there an alternative way I can install tools from the
  Toolshed?  This problem pretty much renders the toolshed unusable for
 me...
 
  On Mon, Jan 5, 2015 at 11:14 AM, John Chilton jmchil...@gmail.com
 wrote:
 
  It is certainly the case that Galaxy should be using the latest
  version of mercurial given a number of high profile bugs with older
  versions. Unfortunately it doesn't seem possible to just drop the new
  version it - there are some API changes that prevent Galaxy from
  loading when doing this and the number of people who can add new eggs
  to Galaxy is low.
 
  I have created a Trello card to track this issue:
 
  https://trello.com/c/9A9uIav0
 
  Let us know if you happen to find a workaround for this issue.
 
  -John
 
 
  On Mon, Dec 22, 2014 at 2:55 PM, Ryan G ngsbioinformat...@gmail.com
  wrote:
  I've been trying to track down why I can't get anything from the
 toolshed
  installed and finally have it figured out.
 
  Whenever I tried to install anything I always got an Error with no
  explanation of what the error was.  After enabling Debug messages into
  the
  log file, I see the error is:
 
  tool_shed.util.hg_util DEBUG 2014-12-22 14:47:48,910 Error cloning
  repository: httpsconnection instance has no attribute '_set_hostport'
 
  I googled around and found out this is a known bug/issue with older
  version
  of Mercurial and was fixed in v3.
 
  I added a line to hg_util.py to see where it picks up hg.  Its using
  version
  2.2.3.  Indeed, one of the eggs downloaded by Galaxy is
 mercurial-2.2.3.
 
  I have the newest version of mercurial installed in my site-packages
  folder
  but I guess that's not what galaxy wants.  So my question is, how do I
  get
  Galaxy to use the latest version of Mercurial?  And, Why did it
 download
  an
  older version?
 
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[galaxy-dev] SGE integration

[Ryan G]

I'm trying to get my instance of Galaxy working with Sun Grid Engine.  The
page https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster is not
100% clear on how to do this but I here's what my job_conf.xml looks like:

?xml version=1.0?
job_conf
plugins
plugin id=local type=runner
load=galaxy.jobs.runners.local:LocalJobRunner workers=4/
plugin id=sge type=runner
load=galaxy.jobs.runners.drmaa:DRMAAJobRunner
!-- Override the $DRMAA_LIBRARY_PATH environment
variable --
param
id=drmaa_library_path/apps/sys/sge/ge2011.11/lib/linux-x64/libdrmaa.so/param
/plugin
/plugins
handlers
handler id=sge/
/handlers
destinations default=sge
destination id=local runner=local /
destination id=sge runner=sge
/destination
/destinations
/job_conf


I tried to submit a job via Galaxy and at first the log files indicated the
shell script got created in the job_working_dir and I was a job ID, but
when the job completed, Galaxy didn't know about it.  Now, I have no jobs
runnings and I can't submit anything via Galaxy.  It doesn't appear to
submit them to SGE or even create the directory for the job.  Pastor.log
doesn't show anything either.  So, I guess I could use a little help with
getting Galaxy running with SGE.  I have a simple set up so nothing fancy.
Any ideas where to get started?
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Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed

[Ryan G]

  stdio
exit_code range=-1 level=fatal description=RandomSubFq failed /
  /stdio


this works.  Thanks.

On Tue, Apr 28, 2015 at 11:51 AM, Dannon Baker dannon.ba...@gmail.com
wrote:

 Like Peter mentions, we did this because historically not all tools used
 (still don't, I guess) exit codes correctly.  If yours does, you can set
 exit_code tags and everything should work.

 On Tue, Apr 28, 2015 at 11:47 AM Ryan G ngsbioinformat...@gmail.com
 wrote:

 ok, thanks.  Let me look at this.  When I look at the information about
 the tool, Galaxy does see the exit code is 0, which I think would be
 sufficient to know the tool ran correctly.


 On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock p.j.a.c...@googlemail.com
 wrote:

 You probably need to set the stdio tag, since due to a
 historical design choice by default any output on stderr
 is treated as an error. See:

 https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

 Peter

 On Tue, Apr 28, 2015 at 4:41 PM, Ryan G ngsbioinformat...@gmail.com
 wrote:
   Hi - I implemented a tool I us into Galaxy but when I run the tool
 view
  Galaxy, Galaxy thinks the tool failed.  I checked the output file the
 tools
  create, and it succeeded.
 
  How do I tell Galaxy that a tool it ran was successful?  Is it
 something in
  my XML file?  The tool is outputting some info to stderr.  Could this
 be
  why?
 
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Re: [galaxy-dev] optional tool arguments

[Ryan G]

Yes it took some experimenting but I finally figured it out. 

Sent from my iPhone

 On Apr 29, 2015, at 4:51 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
 
 Yes, for example:
 https://github.com/peterjc/pico_galaxy/blob/master/tools/seq_filter_by_id/seq_filter_by_id.xml
 
 Peter
 
 On Wed, Apr 29, 2015 at 8:23 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
 Hi Ryan
 
 I guess you can work with filters, see:
 
 https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cdata.3E_tag_set
 
 
 
 Regards, Hans-Rudolf
 
 
 
 
 On 04/28/2015 06:28 PM, Ryan G wrote:
 
 Hi - I'm implementing a new tool in Galaxy.  The tool either takes 1 or
 2 fastq files as input.  If 1 file is specified, then 1 output file is
 created.  If 2 inputs are specified, then 2 output files will be
 created.  How do I specify the optional output parameter?
 
 I'm using this as my tool description right now:
 
 tool id=subsample_fastq name=Random subsample
   descriptiona fastq file/description
   command
 ### Check for optional input file
 #if strlen($fq2)  0:
   RandomSubFq -w $readsRequested -i $fq1 -i $fq2 -o $out1 -o
 $out2
 #else:
   RandomSubFq -w $readsRequested -i $fq1 -o $out1
 #end if
   /command
   inputs
 param name=fq1 type=data format=fastq label=FASTQ file (1st
 of Pair)/
 param name=fq2 type=data format=fastq label=FASTQ file (2nd
 of Pair) optional=true/
 param name=readsRequested type=integer min=1 value=10
 label=Total number of reads you want from the file/
   /inputs
   outputs
 data format=fastq name=out1 /
 data format=fastq name=out2 /
   /outputs
   stdio
 exit_code range=-1 level=fatal description=RandomSubFq failed
 /
   /stdio
 
 
 
 
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Re: [galaxy-dev] Data Libraries

[Ryan G]

We have 4 different people in our sequencing lab each working on different
projects.  Once sequencing is done, they want to be able to create a data
library specific for that project.  Giving them all admin rights is not
what we want, but instead giving them the ability to add data libraries so
that the PI's and analysts can get access to the data is preferable.

Creating one library and allowing them to add subfolders basically forces
all the data into 1 library.  -- won't work.

Having somone with admin rights create a library and give them access to it
could work but isn't preferable as that creates unnecessary steps for an
admin person that isn't really needed.

One only other option is to give them a tool that creates the library for
them, but this is a workaround.


On Fri, Apr 24, 2015 at 7:28 AM, Nicola Soranzo nsora...@tiscali.it wrote:

  You may just use a different folder for each project inside a
 Sequencing library. Would that work?

 Nicola

 Il 24.04.2015 13:10 Ryan G ha scritto:

 This could work.  In the long run though, after sequencing for a project,
 we'd like them people in the sequencing lab to be able to add the data to
 Galaxy in project specific libraries, without having an admin create a
 library for them.

 On Thu, Apr 23, 2015 at 4:56 PM, Martin Čech mar...@bx.psu.edu wrote:

 Hello Ryan,
 it is currently not possible to give users rights to create data
 libraries. However you can create the libraries for them and give them
 rights to create and manage subfolders (doing the same things but one level
 below).
 Would that address your goal?
 Martin

 On Thu, Apr 23, 2015 at 4:33 PM Ryan G ngsbioinformat...@gmail.com
 wrote:

  Hi all - We are trying to use Galaxy as a mechanism for our sequencing
 lab to create data libraries for data they generate.  I noticed in the
 docs, only Admins are able to create data libraries.  Is there a way to
 change this?  I'd like to give specific users in our group this ability
 without giving them admin rights.

 Ryan

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Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed

[Ryan G]

You are correct.  It's always passing even when it fails. There was nothing in 
the docs to indicate a pass. 

Sent from my iPhone

 On Apr 28, 2015, at 3:44 PM, John Chilton jmchil...@gmail.com wrote:
 
 I feel like that stdio tag is going to cause it to always pass - even
 if the exit code is not 0. Am I wrong? I like:
 
  stdio
  exit_code range=1: /
  /stdio
 
 myself. Björn Grüning uses -
 
 stdio
 exit_code range=1: /
 exit_code range=:-1 /
 regex match=Error: /
 regex match=Exception: /
 /stdio
 
 which is a popular choice.
 
 As a heads up for people reading discussion in the future - starting
 in 15.05 - you will be able to just add detect_errors=exit_code on
 the command tag to get a more sensible default behavior.
 https://github.com/galaxyproject/galaxy/pull/117
 
 -John
 
 
 On Tue, Apr 28, 2015 at 12:12 PM, Ryan G ngsbioinformat...@gmail.com wrote:
 stdio
  exit_code range=-1 level=fatal description=RandomSubFq failed /
 /stdio
 
 
 this works.  Thanks.
 
 On Tue, Apr 28, 2015 at 11:51 AM, Dannon Baker dannon.ba...@gmail.com
 wrote:
 
 Like Peter mentions, we did this because historically not all tools used
 (still don't, I guess) exit codes correctly.  If yours does, you can set
 exit_code tags and everything should work.
 
 On Tue, Apr 28, 2015 at 11:47 AM Ryan G ngsbioinformat...@gmail.com
 wrote:
 
 ok, thanks.  Let me look at this.  When I look at the information about
 the tool, Galaxy does see the exit code is 0, which I think would be
 sufficient to know the tool ran correctly.
 
 
 On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock p.j.a.c...@googlemail.com
 wrote:
 
 You probably need to set the stdio tag, since due to a
 historical design choice by default any output on stderr
 is treated as an error. See:
 
 https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
 
 Peter
 
 On Tue, Apr 28, 2015 at 4:41 PM, Ryan G ngsbioinformat...@gmail.com
 wrote:
 Hi - I implemented a tool I us into Galaxy but when I run the tool
 view
 Galaxy, Galaxy thinks the tool failed.  I checked the output file the
 tools
 create, and it succeeded.
 
 How do I tell Galaxy that a tool it ran was successful?  Is it
 something in
 my XML file?  The tool is outputting some info to stderr.  Could this
 be
 why?
 
 ___
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Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed

[Ryan G]

ok, thanks.  Let me look at this.  When I look at the information about the
tool, Galaxy does see the exit code is 0, which I think would be sufficient
to know the tool ran correctly.


On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:

 You probably need to set the stdio tag, since due to a
 historical design choice by default any output on stderr
 is treated as an error. See:

 https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

 Peter

 On Tue, Apr 28, 2015 at 4:41 PM, Ryan G ngsbioinformat...@gmail.com
 wrote:
   Hi - I implemented a tool I us into Galaxy but when I run the tool view
  Galaxy, Galaxy thinks the tool failed.  I checked the output file the
 tools
  create, and it succeeded.
 
  How do I tell Galaxy that a tool it ran was successful?  Is it something
 in
  my XML file?  The tool is outputting some info to stderr.  Could this be
  why?
 
  ___
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[galaxy-dev] Can a tool retrieve a user's API KEY?

[Ryan G]

I'm trying to create a tool that user's can use that will interact with
Galaxy 's API, however the tool needs to be able to determine the user's
API key.Is this possible?  Can a tool determine what the user's API key
is when the user actually runs the tool?
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[galaxy-dev] input dataset(s) and collections

[Ryan G]

Hi all - I'm constructing a wrapper for a tool I have and the input to the
tool can be:

1)  a single fastq file (single end sample)
2)  multiple singled-end fastq files
3)  a single paired-end sample
4)  multiple paired-end samples.

I have cases #1 and #2 handled, however case #3 is presenting a problem.
If the user select Paired-End sample, I want to restrict them to
selecting only a single fastq1 and fastq2 file.

If they want to submit multiple paired-end samples I only want to allow
them to submit them  as a list of dataset pairs.  I can get this part to
work.

I just need to restrict users to selecting only a single fastq1 and fastq2
file when the input_type is Paired-End.

My XML is as follows.  Any help would be appreciated

!-- Input FastQ file(s) --
conditional name=input_type
  param name=input_type_selector type=select label=Select input
type help=Select between single and paired fastq data
option value=singleSingle-End/option
option value=pairedPaired-End/option
option value=paired_collectionPaired Collection/option
  /param
  when value=single
param name=fastq_input1 type=data format=fastq label=Select
fastq dataset multiple=true help=Specify dataset with single end reads
/
  /when
  when value=paired
param name=fastq_input1 type=data format=fastq label=Select
fastq dataset help=Specify dataset with 1st of paired-end reads /
param name=fastq_input2 type=data format=fastq label=Select
fastq dataset help=Specify dataset with 2nd of paired-end reads /
  /when
  when value=paired_collection
param name=fastq_collection type=data_collection
collection_type=list:paired label=Select a paired collection help=See
help section for an explanation of dataset collections/
  /when
/conditional
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Re: [galaxy-dev] input dataset(s) and collections

[Ryan G]

If the user selects mulitple pairs of paired-end data, I want that
submitted the same way as a list of paired-end data.  I don't want a
separate job for each paired-end data.  Rather, I want a single job to
consume the entire list.

It seems to be easier to disable the ability to select multiple fastq1s and
fastq2s, and only allow the user to specify a list of paired-end reads.
This way, I can guarantee the pairs of fastq files match up correctly.

On Thu, Jun 25, 2015 at 10:41 AM, John Chilton jmchil...@gmail.com wrote:

 So you don't want the multi-run options to appear next to these
 inputs? There is currently no way for the tool author to disable this.
 I will admit that I am skeptical this is a good idea, fundamentally is
 feels like tool authors should not be able to prevent end users from
 running the tool multiple times in parallel. Though I will also admit
 in practice there are times this option leads to confusion for users
 about what will actually happen and multiple people have requested an
 option to disable it.


 http://dev.list.galaxyproject.org/Tool-development-Selecting-a-single-item-from-input-dataset-td4666447.html
 https://trello.com/c/qCtBBB8n

 -John


 On Tue, Jun 23, 2015 at 12:58 PM, Ryan G ngsbioinformat...@gmail.com
 wrote:
  Hi all - I'm constructing a wrapper for a tool I have and the input to
 the
  tool can be:
 
  1)  a single fastq file (single end sample)
  2)  multiple singled-end fastq files
  3)  a single paired-end sample
  4)  multiple paired-end samples.
 
  I have cases #1 and #2 handled, however case #3 is presenting a
 problem.  If
  the user select Paired-End sample, I want to restrict them to selecting
  only a single fastq1 and fastq2 file.
 
  If they want to submit multiple paired-end samples I only want to allow
 them
  to submit them  as a list of dataset pairs.  I can get this part to work.
 
  I just need to restrict users to selecting only a single fastq1 and
 fastq2
  file when the input_type is Paired-End.
 
  My XML is as follows.  Any help would be appreciated
 
  !-- Input FastQ file(s) --
  conditional name=input_type
param name=input_type_selector type=select label=Select input
  type help=Select between single and paired fastq data
  option value=singleSingle-End/option
  option value=pairedPaired-End/option
  option value=paired_collectionPaired Collection/option
/param
when value=single
  param name=fastq_input1 type=data format=fastq
 label=Select
  fastq dataset multiple=true help=Specify dataset with single end
 reads
  /
/when
when value=paired
  param name=fastq_input1 type=data format=fastq
 label=Select
  fastq dataset help=Specify dataset with 1st of paired-end reads /
  param name=fastq_input2 type=data format=fastq
 label=Select
  fastq dataset help=Specify dataset with 2nd of paired-end reads /
/when
when value=paired_collection
  param name=fastq_collection type=data_collection
  collection_type=list:paired label=Select a paired collection
 help=See
  help section for an explanation of dataset collections/
/when
  /conditional
 
 
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Re: [galaxy-dev] Custom Tool Dev Questions

[Ryan G]

Ok, Great.  I think I have part of this figured out.  I have a conditional
input as specified:

conditional name=input_type
  param name=input_type_selector type=select label=Select input
type help=Select between single and paired fastq data
option value=singleSingle-End/option
option value=pairedPaired-End/option
option value=paired_collectionPaired Collection/option
  /param
  when value=single
param name=fastq_input1 type=data format=fastq label=Select
fastq dataset multiple=true help=Specify dataset with single end reads
/
  /when
  when value=paired
param name=fastq_input1 type=data format=fastq label=Select
fastq dataset help=Specify dataset with paired-end reads /
param name=fastq_input2 type=data format=fastq label=Select
fastq dataset help=Specify dataset with paired-end reads /
  /when
  when value=paired_collection
param name=fastq_collection type=data_collection
collection_type=list:paired label=Select a paired collection help=See
help section for an explanation of dataset collections/
  /when
/conditional


In my command section, I want to test how this is passed to the tool, so
I have:

  command

#if str( $input_type.input_type_selector ) == single:

  echo Input Type: Single
  echo Input File: $input_type.fastq_input1

#elif str( $input_type.input_type_selector ) == paired:

  echo Input Type: Paired
  echo FastQ1: $input_type.fastq_input1\nFastQ2:
$input_type.fastq_input2

#elif str( $input_type.input_type_selector ) == paired_collection:

  print Input Type: Collection\n
  #for $element in $input_type.$fastq_collection:

echo FastQ1: $element.fastq_input1

  #end for

#end if

  /command

The single and paired works as expected, however I can select multiple
input for paired which I don't want to allow.  A user should only be able
to select a single pair of fastq files.  To select multiple pairs, I have
paired_collection.

The second problem is in the command section, I'm trying to iterated
through the pair of inputs, however my echo statement is causing a Cheetah
error.  I tried different incarnations of it as well.  My latest (and what
I thought correct) is shown above.  It generates the error:

Traceback (most recent call last):
  File 
/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/jobs/runners/__init__.py,
line 163, in prepare_job
job_wrapper.prepare()
  File /apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/jobs/__init__.py,
line 858, in prepare
self.command_line, self.extra_filenames = tool_evaluator.build()
  File /apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/tools/evaluation.py,
line 411, in build
self.__build_command_line( )
  File /apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/tools/evaluation.py,
line 427, in __build_command_line
command_line = fill_template( command, context=param_dict )
  File /apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/util/template.py,
line 9, in fill_template
return str( Template( source=template_text, searchList=[context] ) )
  File 
/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py,
line 1004, in __str__
return getattr(self, mainMethName)()
  File cheetah_DynamicallyCompiledCheetahTemplate_1434732603_97_56713.py,
line 107, in respond
AttributeError: 'dict' object has no attribute 'VFFSL'

How do I iterate through the fastq inputs when they are passed as a list:paired?



On Fri, Jun 19, 2015 at 11:31 AM, John Chilton jmchil...@gmail.com wrote:

 The option in the GUI for selecting multiple datasets for a single
 data parameter - causes multiple jobs to be created as you noted. If
 you just place multiple=true on your data input parameter  - that
 button will go away and all the datasets will be used for a single
 job.

 If your tool consumes pairs of datasets - you will want to expose an
 option where you are using a parameter like:

 input name=input_pairs type=data_collection
 collection_type=list:paired format=fastq /

 and then your users will have to use the data collection creator to
 pair off the datasets into a big list before using your tool - but the
 creator is actually really nice - I think it makes it very easy to
 build large lists of pairs.

 Hope this helps - happy to provide more details,
 -John

 On Fri, Jun 19, 2015 at 11:24 AM, Ryan G ngsbioinformat...@gmail.com
 wrote:
  Hi all - I have a tool which is essentially an entire NGS pipeline
 bundled
  into a perl script and associated modules.  I'd like to offer this tool
 to
  users via Galaxy.
 
  I'm trying to pass a bunch of fastq files to the tool, but noticed that
  operating on multiple datasets creates a separate job for each dataset.
 I
  want to pass all the datasets to the tool so only one galaxy job is
 actually
  created.  Is this possible, and if so, how do I go about doing this?
 
  Ryan

Re: [galaxy-dev] Galaxy API to upload files to data library

[Ryan G]

What is HDA?

Sent from my iPhone

 On Jun 26, 2015, at 1:10 PM, Martin Čech mar...@bx.psu.edu wrote:
 
 Hello Ryan,
 
 for interacting with libraries through the Bioblend:
 http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.libraries
 
 for loading data to libraries form the Galaxy's system (e.g. after FTP 
 upload, or when admin):
 https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/lda_datasets.py#L401
 
 for uploading new files or importing from HDA:
 https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/library_contents.py#L144
 
 Hope this helps.
 
 M.
 
 On Fri, Jun 26, 2015 at 12:56 PM Ryan G ngsbioinformat...@gmail.com wrote:
 By browsing the api code, I discovered library_contents.py that looks like 
 it should be used.  Why this and not folder_contents.py?  There seems to be 
 overlap of these two.  I would expect to upload files to folders within 
 libraries...
 
 
 On Thu, Jun 25, 2015 at 2:43 PM, Ryan G ngsbioinformat...@gmail.com wrote:
 Hi all - I'm trying to figure out how to script the ability to upload data 
 (fastq) files to Galaxy via the API.
 
 I can get the Library's root_folder_id, but am unsure of what the API call 
 is to upload a file.  I'm constructing this dictionary:
 
 data = {}
 data['folder_id'] = galaxyFolderId
 data['create_type'] = 'file'
 data['file_type'] = 'fastq'
 data['upload_option'] = 'upload_paths'
 data['filesystem_paths'] = fileToUpload
 data['link_data_only'] = 'link_to_files'
 
 I assume this is the correct format based on other code I've seen, but I'm 
 not sure what the actual submit call should be. 'api/libraries/' or 
 'api/folders'
 
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Re: [galaxy-dev] Galaxy API to upload files to data library

[Ryan G]

What if the data is not in the history?   Ie we received ngs data from an 
external source and copied it to a location on our server.  I now want to link 
to it in Galaxy. 

What I was doing previously was entering the file system path through the UX 
but we want to automate this a bit and have a script scan Various directories 
and import all the *.fastq.gz files while preserving the directory structure.  
I have most of the script written but just need to figure out how to link to 
the datasets. 

Sent from my iPhone

 On Jun 26, 2015, at 1:24 PM, Martin Čech mar...@bx.psu.edu wrote:
 
 History Dataset Association. i.e. if you already have the dataset in history 
 you can very easily import it to a data library.
 
 M.
 
 On Fri, Jun 26, 2015 at 1:23 PM Ryan G ngsbioinformat...@gmail.com wrote:
 What is HDA?
 
 Sent from my iPhone
 
 On Jun 26, 2015, at 1:10 PM, Martin Čech mar...@bx.psu.edu wrote:
 
 Hello Ryan,
 
 for interacting with libraries through the Bioblend:
 http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.libraries
 
 for loading data to libraries form the Galaxy's system (e.g. after FTP 
 upload, or when admin):
 https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/lda_datasets.py#L401
 
 for uploading new files or importing from HDA:
 https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/library_contents.py#L144
 
 Hope this helps.
 
 M.
 
 On Fri, Jun 26, 2015 at 12:56 PM Ryan G ngsbioinformat...@gmail.com 
 wrote:
 By browsing the api code, I discovered library_contents.py that looks like 
 it should be used.  Why this and not folder_contents.py?  There seems to 
 be overlap of these two.  I would expect to upload files to folders within 
 libraries...
 
 
 On Thu, Jun 25, 2015 at 2:43 PM, Ryan G ngsbioinformat...@gmail.com 
 wrote:
 Hi all - I'm trying to figure out how to script the ability to upload 
 data (fastq) files to Galaxy via the API.
 
 I can get the Library's root_folder_id, but am unsure of what the API 
 call is to upload a file.  I'm constructing this dictionary:
 
 data = {}
 data['folder_id'] = galaxyFolderId
 data['create_type'] = 'file'
 data['file_type'] = 'fastq'
 data['upload_option'] = 'upload_paths'
 data['filesystem_paths'] = fileToUpload
 data['link_data_only'] = 'link_to_files'
 
 I assume this is the correct format based on other code I've seen, but 
 I'm not sure what the actual submit call should be. 'api/libraries/' or 
 'api/folders'
 
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[galaxy-dev] bowtie dataset pair input

[Ryan G]

Hi all - It looks like bowtie's wrapper is working incorrectly for a list
of dataset pairs.  Its expecting all the forward reads in one dataset list
and the reverse reads in a separate dataset list.

Instead, I have a list of dataset pairs (for paired-end data).  This cannot
be provided to bowtie as input.  If I correct this, should I create a pull
request for it?  Alternatively, does someone already have a corrected
version of this?
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Re: [galaxy-dev] functional tests / database lock

[Ryan G]

I am using postgres in production but want to validate my staging instance
before pushing it into production.  I do this with the functional tests.  I
guess I'll have to set up a postgres database for the staging instance as
well.


On Mon, Jun 15, 2015 at 10:32 AM, John Chilton jmchil...@gmail.com wrote:

 Not exactly - I feel like sqlite should be able to do the kinds of
 things Galaxy does without this occurring - it should just be
 inefficient. We are probably doing something across multiple threads
 that we should not be - presumably related to job handling. After a
 recent sqlalchemy upgrade - there is now a new error message in the
 logs that should help track down the problem:

 sqlalchemy.pool.NullPool ERROR 2015-06-15 09:53:47,547 Exception
 during reset or similar
 Traceback (most recent call last):
   File build/bdist.linux-x86_64/egg/sqlalchemy/pool.py, line 571, in
 _finalize_fairy
 fairy._reset(pool)
   File build/bdist.linux-x86_64/egg/sqlalchemy/pool.py, line 705, in
 _reset
 pool._dialect.do_rollback(self)
   File build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py,
 line 412, in do_rollback
 dbapi_connection.rollback()
 ProgrammingError: SQLite objects created in a thread can only be used
 in that same thread.The object was created in thread id
 140442561648384 and this is thread id 140442989479680

 At any rate - we recommend using postgres in production for a reason -
 these sqlite errors are pretty common.

 -John


 On Fri, Jun 12, 2015 at 11:15 AM, Ryan G ngsbioinformat...@gmail.com
 wrote:
  Is there a known cause for this?
 
  On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo nsora...@tiscali.it
  wrote:
 
  Hi Ryan,
  there is no know fix for this, apart from moving to PostgreSQL.
 
  Cheers,
  Nicola
 
  Il 12.06.2015 16:43 Ryan G ha scritto:
 
  Hi all - I'm running functional tests on a set of tools using
  'run_tests.sh -sid ...'.  A few of the tests fail.  When I go back and
 run
  the tool tests individually, they succeed.  So I looked into why they
 fail
  when running them in batch, and it turns out to be a database lock.  I'm
  using the default sqllite database that run_tests.sh creates.  Does this
  need to be tuned somehow?
 
 
  galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched
  Error - : (OperationalError) database is locked u'SELECT api_keys.id AS
  api_keys_id, api_keys.create_time AS api_keys_create_time,
 api_keys.user_id
  AS api_keys_user_id, api_keys.key AS api_keys_key \nFROM api_keys
 \nWHERE
  api_keys.key = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',)
  URL:
 
 http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746714beb6212bc8
  File
 
 '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py',
  line 149 in __call__
app_iter = self.application(environ, sr_checker)
  File
 
 '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
  line 84 in __call__
return self.application(environ, start_response)
  File
 
 '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
  line 633 in __call__
return self.application(environ, start_response)
  File
 
 '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py',
  line 132 in __call__
return self.handle_request( environ, start_response )
  File
 
 '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py',
  line 159 in handle_request
trans = self.transaction_factory( environ )
  File
 
 '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
  line 71 in
self.set_transaction_factory( lambda e: self.transaction_chooser( e,
  galaxy_app, session_cookie ) )
  File
 
 '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
  line 102 in transaction_chooser
return GalaxyWebTransaction( environ, galaxy_app, self,
 session_cookie )
  File
 
 '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
  line 194 in __init__
self.error_message = self._authenticate_api( session_cookie )
  File
 
 '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py',
  line 283 in _authenticate_api
provided_key = self.sa_session.query( self.app.model.APIKeys ).filter(
  self.app.model.APIKeys.table.c.key == api_key ).one()
  File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2184
 in
  one
  File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2227
 in
  __iter__
  File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2242
 in
  _execute_and_instances
  File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1449
  in execute
  File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1584
  in _execute_clauseelement
  File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1698
  in _execute_context
  File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py

[galaxy-dev] keep job output and scripts on failed tests

[Ryan G]

I'd like to recommend a change.  If jobs fail to run during functional
tests, I'd like to keep the failed job files around to be examined.  I
added the following to do so:

+++ scripts/functional_tests.py
@@ -372,6 +372,7 @@ def main():
user_library_import_dir=user_library_import_dir,
master_api_key=master_api_key,
use_tasked_jobs=True,
+   cleanup_job='onsuccess'
 )
 if install_database_connection is not None:
 kwargs[ 'install_database_connection' ] =
install_database_connection
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[galaxy-dev] picard_MarkDuplicatesWithMateCigar functional test failure

[Ryan G]

The functional test for this tool fails.  Looking at the XML wrapper, it
looks like $comments is invalidit doesn't exist anywhere else in the
xml file.  I know that comments can be specified multiple times however
there is no way to get the comments fields to appear multiple times in the
UI as far as I can tell.  So, I changed it from

#for $element in $comments:
  COMMENT=${element.comment}
#end for

to

COMMENT=${comment}

and the functional test passes.
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Re: [galaxy-dev] keep job output and scripts on failed tests

[Ryan G]

I tried that and the directories don't get removed however the job files
still get deleted.

On Fri, Jun 12, 2015 at 12:03 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:

 Hi Ryan,

 Something very handy for tool developers running functional tests
 is if the environment variable GALAXY_TEST_NO_CLEANUP
 is set, run_tests.sh shouldn't remove the test output.

 This is great when debugging why a test is failing.

 Peter


 On Fri, Jun 12, 2015 at 4:29 PM, Ryan G ngsbioinformat...@gmail.com
 wrote:
  I'd like to recommend a change.  If jobs fail to run during functional
  tests, I'd like to keep the failed job files around to be examined.  I
 added
  the following to do so:
 
  +++ scripts/functional_tests.py
  @@ -372,6 +372,7 @@ def main():
  user_library_import_dir=user_library_import_dir,
  master_api_key=master_api_key,
  use_tasked_jobs=True,
  +   cleanup_job='onsuccess'
   )
   if install_database_connection is not None:
   kwargs[ 'install_database_connection' ] =
  install_database_connection
 
 
 
 
 
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Re: [galaxy-dev] picard_MarkDuplicatesWithMateCigar functional test failure

[Ryan G]

done

On Fri, Jun 12, 2015 at 11:33 AM, Nicola Soranzo nsora...@tiscali.it
wrote:

  Hi Ryan,
 please open a pull request at
 https://github.com/galaxyproject/tools-devteam

 The file is in tools/picard/ directory.

 Thanks,
 Nicola

 Il 12.06.2015 17:23 Ryan G ha scritto:

  The functional test for this tool fails.  Looking at the XML wrapper, it
 looks like $comments is invalidit doesn't exist anywhere else in the
 xml file.  I know that comments can be specified multiple times however
 there is no way to get the comments fields to appear multiple times in the
 UI as far as I can tell.  So, I changed it from

 #for $element in $comments:
   COMMENT=${element.comment}
 #end for

 to

 COMMENT=${comment}

 and the functional test passes.








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[galaxy-dev] minor visual bug found when using Firefox

[Ryan G]

In the workflow editor, if you add an Input dataset collection, the
Collection Type: shows list.  No dropdown arrow appears using Firefox.  A
dropdown arrow appears when you mouse over using Chrome.

In Firefox, if you mouse over where the dropdown box should be, you can
still click to choose list of datasets...

For the longest time, I thought this was broken until a co-worker showed me
it works with Chrome.  I'd make a Trello card for this but I can't access
Trello from behind the company firewall
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Re: [galaxy-dev] Galaxy API to upload files to data library

[Ryan G]

Perfect.  Thanks!

On Fri, Jun 26, 2015 at 6:02 PM, Martin Čech mar...@bx.psu.edu wrote:

 The second link leads to an endpoint that does exactly that.
 M.


 On Fri, Jun 26, 2015 at 4:43 PM Ryan G ngsbioinformat...@gmail.com
 wrote:

 What if the data is not in the history?   Ie we received ngs data from an
 external source and copied it to a location on our server.  I now want to
 link to it in Galaxy.

 What I was doing previously was entering the file system path through the
 UX but we want to automate this a bit and have a script scan Various
 directories and import all the *.fastq.gz files while preserving the
 directory structure.  I have most of the script written but just need to
 figure out how to link to the datasets.

 Sent from my iPhone

 On Jun 26, 2015, at 1:24 PM, Martin Čech mar...@bx.psu.edu wrote:

 History Dataset Association. i.e. if you already have the dataset in
 history you can very easily import it to a data library.

 M.

 On Fri, Jun 26, 2015 at 1:23 PM Ryan G ngsbioinformat...@gmail.com
 wrote:

 What is HDA?

 Sent from my iPhone

 On Jun 26, 2015, at 1:10 PM, Martin Čech mar...@bx.psu.edu wrote:

 Hello Ryan,

 for interacting with libraries through the Bioblend:

 http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.libraries

 for loading data to libraries form the Galaxy's system (e.g. after FTP
 upload, or when admin):

 https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/lda_datasets.py#L401

 for uploading new files or importing from HDA:

 https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/library_contents.py#L144

 Hope this helps.

 M.

 On Fri, Jun 26, 2015 at 12:56 PM Ryan G ngsbioinformat...@gmail.com
 wrote:

 By browsing the api code, I discovered library_contents.py that looks
 like it should be used.  Why this and not folder_contents.py?  There seems
 to be overlap of these two.  I would expect to upload files to folders
 within libraries...


 On Thu, Jun 25, 2015 at 2:43 PM, Ryan G ngsbioinformat...@gmail.com
 wrote:

 Hi all - I'm trying to figure out how to script the ability to upload
 data (fastq) files to Galaxy via the API.

 I can get the Library's root_folder_id, but am unsure of what the API
 call is to upload a file.  I'm constructing this dictionary:

 data = {}
 data['folder_id'] = galaxyFolderId
 data['create_type'] = 'file'
 data['file_type'] = 'fastq'
 data['upload_option'] = 'upload_paths'
 data['filesystem_paths'] = fileToUpload
 data['link_data_only'] = 'link_to_files'

 I assume this is the correct format based on other code I've seen, but
 I'm not sure what the actual submit call should be. 'api/libraries/' or
 'api/folders'


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[galaxy-dev] Galaxy in Amazon

[Ryan G]

Hi all - We are running a local instance of Galaxy on our internal
infrastructure.  It seems to be going well.

We've gotten to the point where we are ready to migrate our NGS data to
Amazon for storage in S3.  We are also looking at how Galaxy can be used in
Amazon.  Specifically, we are interested in understanding:

1)  Should we run an instance of Galaxy in Amazon, or continue to run it
locally (to minimize costs) but have it run analyses in Amazon?

2)  Regardless of how we run it, data will be stored in S3.  How will
Galaxy interact with S3 for its Data Libraries?

3)  Is it even possible to separate the Galaxy web interface from the HPC
cluster?

3)  We understand Galaxy in Amazon uses CloudMan.  Can we run this in our
VPC with our own AMI?

If anyone can provide insights into how they are using Galaxy in Amazon, I
am very interested to hear your thoughts.

Ryan
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[galaxy-dev] Workflow editor stuck on loading workflow

[Ryan G]

It looks like a recent commit since 6/26 to 15.05 is break the workflow
editor.  I have a pipeline I'm trying to edit.  I updated my instance of
Galaxy and now when I try to edit a workflow, the editor is stuck at
Loading workflow editor.
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Re: [galaxy-dev] Error sorting or uploading Bam File

[Ryan G]

I would think the correct approach would be to allow any bam file and if a tool 
requires a coordinate sorted bam and one is not provided it would make sense 
for the tool to fail with an error.   

Does galaxy itself require a coordinate sorted bam or this this so the majority 
of tools can function properly?

Sent from my iPhone

 On Jul 17, 2015, at 11:08 AM, John Chilton jmchil...@gmail.com wrote:
 
 I'm not the right person to respond to this but since no one else has
 I will explain my limited (probably incorrect) understanding of the
 problem and what needs to be done. I believe Galaxy assumes all bam
 files are coordinated sorted by default - so Galaxy's bam datatype
 would be better thought of as a coordinate-sorted bam. Certain people
 do not want to allow non-coordinate sorted bam files because these
 would be allowed by Galaxy as valid as inputs to tools that expect
 sorted bams - and things would break. For the same reason I imagine
 these people would argue the bai file needs to be generated because
 certain tools will depend on its existence.
 
 I believe the proposed solution is to add an unsorted bam datatype to
 Galaxy. I don't know if there is any work in progress on this but it
 seems to be needed by many researchers.
 
 Hope this clarifies things somewhat,
 -John
 
 
 On Mon, Jun 29, 2015 at 11:06 AM, julie dubois dubju...@gmail.com wrote:
 Hi all,
 
 My galaxy is the last update and I work with samtools 1.2.
 I have a bug with the sorting and the upload of bam file.
 This bug appears only when I try to upload bam sorted by name or when
 I try to sort by name.
 When I work with bam sorted by coordinate, there is no problem.
 
 So, when I try to sort a bam file by name, this error appears under
 the bug icon :
 
 Tool execution generated the following error message:
 [bam_sort_core] merging from 20 files...
 *** Error in `python': double free or corruption (!prev): 0x02897990 
 ***
 Aborted (core dumped)
 
 The tool produced the following additional output:
 
 [E::hts_idx_push] chromosome blocks not continuous
 Galaxy attempted to build the BAM index with samtools 1.0+ but failed:
 [Errno 2] No such file or directory:
 '/data/galaxy-dist/database/job_working_directory/024/24109/__dataset_48619_metadata_temp_file_MqhjBN.bai'
 
 And the same type of error appears when I try to upload bam sorted by name.
 
 
 What I understand is that the bam can be sorted properly (The command
 line to sort is ok in a terminal with no bug and I can follow this
 step in the job_working_directory during the run) but Galaxy seems to
 fail to create a bai.
 
 For our analysis pipeline, I think the bai is not crucial, is it
 possible to avoid this creation of bai during uploading and sorting of
 bam file by name ?
 
 Is there another problem than this creation of bai ?
 
 Thanks.
 
 Julie
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Re: [galaxy-dev] Workflow editor stuck on loading workflow

[Ryan G]

The error I see is TypeError: c.effectiveMapOver is not a function in
static/scripts/galaxy.workflow_editor.canvas.js?v=1436897004

On Tue, Jul 14, 2015 at 4:50 PM, Björn Grüning bjoern.gruen...@gmail.com
wrote:

 Hi Ryan,

 try to look at the JS console. I suspect some problem with one of the
 tools in your workflow.

 Cheers,
 Bjoern

 Am 14.07.2015 um 22:02 schrieb Ryan G:
  Hmmm this only happens on a specific workflow.  How can I debug this?
 
  On Tue, Jul 14, 2015 at 3:37 PM, Ryan G ngsbioinformat...@gmail.com
 wrote:
 
  It looks like a recent commit since 6/26 to 15.05 is break the workflow
  editor.  I have a pipeline I'm trying to edit.  I updated my instance of
  Galaxy and now when I try to edit a workflow, the editor is stuck at
  Loading workflow editor.
 
 
 
 
 
 
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[galaxy-dev] tabular file displayed without tabs

[Ryan G]

Hi - I have a tools that generates a tab-delimited text file as output.
when I click the eye icon to view the data, all the fields are compressed
as if there were no tabs.  If I expand the history view, the little preview
window shows the contents as tabbed.  I've verified that the spaces are
indeed '\t' tab characters.  Why would Galaxy not display this file as a
tab-delimited file?
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Re: [galaxy-dev] tabular file displayed without tabs

[Ryan G]

The file is an output from a tool and in the tool's xml, its format is
tabular.



On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning <bjoern.gruen...@gmail.com>
wrote:

> Hi Ryan,
>
> is it recognised as 'tabular'?
>
> Ciao,
> Bjoern
>
> Am 27.10.2015 um 04:42 schrieb Ryan G:
> > Hi - I have a tools that generates a tab-delimited text file as output.
> > when I click the eye icon to view the data, all the fields are compressed
> > as if there were no tabs.  If I expand the history view, the little
> preview
> > window shows the contents as tabbed.  I've verified that the spaces are
> > indeed '\t' tab characters.  Why would Galaxy not display this file as a
> > tab-delimited file?
> >
> >
> >
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> >
>
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[galaxy-dev] Cloudman vs StarCluster

[Ryan G]

Hi all - Our organization requires us to use a specific AMI (with a
specific flavor of linux) that isn't supported by Cloudman.  Its taking us
a bit of time to get this combination working.

Its taken more than 3 weeks and we still don't have Galaxy /  Cloudman
running.  I could probably do the same thing with StarCluster and be up and
running within a day.

I'm very comfortable with using StarCluster and am wondering if there is
any benefit to using Cloudman over StarCluster for node management with
Galaxy.

Thoughts?
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Re: [galaxy-dev] feature request

[Ryan G]

Thanks.

On Mon, Nov 9, 2015 at 4:40 PM, Martin Čech <mar...@bx.psu.edu> wrote:

> Created it for you here:
> https://github.com/galaxyproject/galaxy/issues/1045
>
>
> On Mon, Nov 9, 2015 at 4:39 PM Ryan G <ngsbioinformat...@gmail.com> wrote:
>
>> Yes, I'll do it there.
>>
>> On Mon, Nov 9, 2015 at 4:38 PM, Björn Grüning <bjoern.gruen...@gmail.com>
>> wrote:
>>
>>> Hi Ryan,
>>>
>>> can you create a github issue with this suggestion :)
>>>
>>> Thanks,
>>> Bjoern
>>>
>>> Am 09.11.2015 um 22:37 schrieb Ryan G:
>>> > I'd put this into Trello, but Trello is blocked from my place of
>>> business...
>>> >
>>> > I have a data library with over 200 files in it.  Half of them are
>>> > "clipped" and the other half are not.  I'd like to be able to search
>>> and
>>> > display a subset of files in the data library.  This will make
>>> selecting
>>> > the files I want to import into my history much easier.
>>> >
>>> >
>>> >
>>> > ___
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>>> >   http://galaxyproject.org/search/mailinglists/
>>> >
>>>
>>
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[galaxy-dev] feature request

[Ryan G]

I'd put this into Trello, but Trello is blocked from my place of business...

I have a data library with over 200 files in it.  Half of them are
"clipped" and the other half are not.  I'd like to be able to search and
display a subset of files in the data library.  This will make selecting
the files I want to import into my history much easier.
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Re: [galaxy-dev] feature request

[Ryan G]

Yes, I'll do it there.

On Mon, Nov 9, 2015 at 4:38 PM, Björn Grüning <bjoern.gruen...@gmail.com>
wrote:

> Hi Ryan,
>
> can you create a github issue with this suggestion :)
>
> Thanks,
> Bjoern
>
> Am 09.11.2015 um 22:37 schrieb Ryan G:
> > I'd put this into Trello, but Trello is blocked from my place of
> business...
> >
> > I have a data library with over 200 files in it.  Half of them are
> > "clipped" and the other half are not.  I'd like to be able to search and
> > display a subset of files in the data library.  This will make selecting
> > the files I want to import into my history much easier.
> >
> >
> >
> > ___
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> >
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> >
>
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[galaxy-dev] User API keys with External (LDAP) authentication disabled?

[Ryan G]

Hi all - I have external authentication established with our enterprise
wide LDAP working with Galaxy.  I just noticed that I can no longer manage
API keys for users from the Admin Page -> API Keys.  I get "Access to
Galaxy user controls is disabled.  User controls are disabled when Galaxy
is configured for external authentication"

We basically have a 'nobody' user in Galaxy that populates the Data Library
with new data from a proprietary system.  We were using a user's API key
(mine) to do this but want to switch over to a daemon style user key.  In
order to do so, I need to generate an API key for the dummy user.

Is there no way to get API keys from the Admin interface with external
authentication?
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Re: [galaxy-dev] external authentication - empty REMOTE_USER

[Ryan G]

I just recently submitted a patch that will display all the environment 
variables being passed to Galaxy in pastor.log.  That should help you determine 
if the variables are set and to what. 


Please excuse any typos -- Sent from my iPhone

> On Oct 21, 2015, at 6:11 AM, Floreline TOUCHARD 
>  wrote:
> 
> Hi,
> 
> I've got an issue with my external authentication configuration. I use Apache 
> and the mod_perl
> 
> modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with NIS 
> accounts.
> 
> I have the authentication form  when I try to access galaxy web page. 
> But after a successful authentication it seems that the REMOTE_USER variable 
> is not passed to my galaxy instance. I'm connected under "@example.org" 
> regardless of the authentication account. That's why I think the REMOTE_USER 
> passed to Galaxy is not 'null' but empty.
> 
> I tested the value of the variable with the following php script:
> 
>  foreach($_SERVER as $key_name => $key_value) {
> print $key_name . " = " . $key_value . "";
> 
> }
> 
> ?>
> 
> I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
> 
> I don't understand where my problem lies.
> 
>  
> 
> Here is my galaxy.conf file :
> 
> Listen 2208
> 
> 
> 
> 
> RewriteEngine on
> DocumentRoot "/path/to/static"
>
> 
>
> 
> Options +Indexes FollowSymLinks MultiViews
> AllowOverride None
> Order allow,deny
> Allow from all
> 
> 
> AuthType Basic
> AuthName "Authentifiez vous"
> PerlAuthenHandler Apache2::AuthenNIS
> PerlAuthzHandler Apache2::AuthzNIS
> PerlSetVar AllowAlternateAuth no
> require valid-user
> 
> 
>
> 
> 
> RewriteEngine on
> RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}]
> RequestHeader set REMOTE_USER %{RU}e
>
> 
> 
>RewriteRule ^/galaxy$ /galaxy/ [R]
>RewriteRule ^/static/style/(.*) /path/to/static/june_2007_style/blue/$1 [L]
>RewriteRule ^/static/scripts/(.*) 
> /softhpc/galaxy/test/galaxy-master/static/scripts/packed/$1
> 
> [L]
>RewriteRule ^/static/(.*) /path/to/static/$1 [L]
>RewriteRule ^/favicon.ico /path/to/static/favicon.ico [L]
>RewriteRule ^/robots.txt /path/to/static/robots.txt [L]
>RewriteRule ^(.*) http://localhost:2209$1 [P]
> 
> 
> 
> 
> 
> Thanks in advance !
> 
> F.T
> 
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Re: [galaxy-dev] external authentication - empty REMOTE_USER

[Ryan G]

Here is the pull request:  https://github.com/galaxyproject/galaxy/pull/823

You can see what file was edited

On Wed, Oct 21, 2015 at 8:40 AM, Floreline TOUCHARD <
floreline.touch...@gmail.com> wrote:

> Thank you ! Can you tell me which files are to update or download ?
> I installed my application on a server that was not open to the outside.
> Currently I do not support different versions or updates of my application
> with git.
> I can download the files to edit and transfer them to the server but not
> to update the entire application at the moment.
>
> F. T
> Le 21 oct. 2015 12:11 PM, "Floreline TOUCHARD" <
> floreline.touch...@gmail.com> a écrit :
>
>> Hi,
>>
>> I've got an issue with my external authentication configuration. I use
>> Apache and the mod_perl
>>
>> modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with
>> NIS accounts.
>>
>> I have the authentication form  when I try to access galaxy web page.
>> But after a successful authentication it seems that the REMOTE_USER
>> variable is not passed to my galaxy instance. I'm connected under "@
>> example.org" regardless of the authentication account. That's why I
>> think the REMOTE_USER passed to Galaxy is not 'null' but empty.
>>
>> I tested the value of the variable with the following php script:
>>
>> > foreach($_SERVER as $key_name => $key_value) {
>> print $key_name . " = " . $key_value . "";
>>
>> }
>>
>> ?>
>>
>> I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
>>
>> I don't understand where my problem lies.
>>
>>
>>
>> Here is my galaxy.conf file :
>>
>> Listen 2208
>>
>> 
>>
>>
>> RewriteEngine on
>> DocumentRoot "/path/to/static"
>>
>>
>>
>>
>> Options +Indexes FollowSymLinks MultiViews
>> AllowOverride None
>> Order allow,deny
>> Allow from all
>>
>>
>> AuthType Basic
>> AuthName "Authentifiez vous"
>> PerlAuthenHandler Apache2::AuthenNIS
>> PerlAuthzHandler Apache2::AuthzNIS
>> PerlSetVar AllowAlternateAuth no
>> require valid-user
>>
>>
>>
>>
>>
>> RewriteEngine on
>> RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}]
>> RequestHeader set REMOTE_USER %{RU}e
>>
>>
>>
>>RewriteRule ^/galaxy$ /galaxy/ [R]
>>RewriteRule ^/static/style/(.*)
>> /path/to/static/june_2007_style/blue/$1 [L]
>>RewriteRule ^/static/scripts/(.*)
>> /softhpc/galaxy/test/galaxy-master/static/scripts/packed/$1
>>
>> [L]
>>RewriteRule ^/static/(.*) /path/to/static/$1 [L]
>>RewriteRule ^/favicon.ico /path/to/static/favicon.ico [L]
>>RewriteRule ^/robots.txt /path/to/static/robots.txt [L]
>>RewriteRule ^(.*) http://localhost:2209$1 [P]
>>
>>
>> 
>>
>>
>> Thanks in advance !
>>
>> F.T
>>
>
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Re: [galaxy-dev] External User Authenticaion

[Ryan G]

Sorry, maybe I'm not being clear.

Galaxy is listening on http://galaxy.mycompany.com:8080

Users access Galaxy via http://mycompay.com/galaxy

If users go to http://galaxy.mycompany.com:8080, they get the External
Authentication message.  From here I want them to be redirected to
http://mycompay.com/galaxy which is where they will be authenticated.

Users never see http://galaxy.mycompany.com:8080they will always see
http://mycompay.com/galaxy



On Tue, Oct 13, 2015 at 12:36 PM, Eric Rasche <e...@tamu.edu> wrote:

>
>
> On 10/13/2015 11:34 AM, Ryan G wrote:
> > We have Apache set up to authenticate users off our LDAP.  If they
> > authenticate correctly, they are then forwarded on through the proxy.
>
> So, mod_auth_ldap? Or not? You say "forwarded" so I'm thinking you may
> not mean this.
>
> >
> > What I want is to prevent users from hitting the galaxy URL directly.
> > If they, do I want to automatically redirect them to the proxy.
>
> Under mod_auth_ldap this should be done for you.
>
> (Worst case scenario you could write some mod_rewrite logic that checks
> for the remote_user header and returns a 301 if it's missing with the
> location of your login page)
>
> >
> >
> > On Tue, Oct 13, 2015 at 11:10 AM, Eric Rasche <e...@tamu.edu
> > <mailto:e...@tamu.edu>> wrote:
> >
> > Hi Ryan,
> >
> > On 10/13/2015 09:50 AM, Ryan G wrote:
> > > Hi all - In regards to external user authentication that I have
> working
> > > now (see thread below).  When users try to go to the actual Galaxy
> page,
> > > they get the message:
> > >
> > >
> > > Access to Galaxy is denied
> >
> > That's expected for External User Auth if you don't have the
> REMOTE_USER
> > header set properly.
> >
> > >
> > > Galaxy is configured to authenticate users via an external method
> (such
> > > as HTTP authentication in Apache), but no shared secret key was
> provided
> > > by the upstream (proxy) server.
> > >
> > > Please contact your local Galaxy administrator. The variable
> > > |remote_user_secret| and |GX_SECRET| header must be set before you
> may
> > > access Galaxy.
> > >
> > >
> > >
> > > That's fine and all but I'd like to have them redirected to the
> real
> > > login page.  Is there a way to do this?  I didn't see anything
> obvious
> > > and was thinking of adding a parameter to galaxy.ini and have
> Galaxy
> > > automatically forward them after 5 seconds or so.
> >
> > What external auth mechanism are you using?
> >
> > >
> > > Ryan
> > >
> > >
> > > On Tue, Oct 13, 2015 at 10:49 AM, Ryan G <
> ngsbioinformat...@gmail.com <mailto:ngsbioinformat...@gmail.com>
> > > <mailto:ngsbioinformat...@gmail.com  ngsbioinformat...@gmail.com>>>
> > wrote:
> > >
> > > Hi all - In regards to external user authentication that I have
> > > working now (see thread below).  When users try to go to the
> actual
> > > Galaxy page, they get the message:
> > >
> > >
> > > On Thu, Oct 1, 2015 at 4:10 PM, Ryan G <
> ngsbioinformat...@gmail.com <mailto:ngsbioinformat...@gmail.com>
> > > <mailto:ngsbioinformat...@gmail.com  ngsbioinformat...@gmail.com>>>
> > wrote:
> > >
> > > I finally got around to this and all is working well.  I
> > > submitted 2 patches to remoteuser.py to assist in debugging
> > > incorrect set ups.
> > >
> > > Last question - When a user logs out, they get the page
> ""Access
> > > to Galaxy user controls is disabled".  I've set the
> > > remote_user_logout_href parameter to a different website,
> but
> > > they still get the "Access to Galaxy user controls is
> disabled".
> > >
> > > I see it in lib/galaxy/webapps/galaxy/controllers/user.py,
> but I
> > > think at that point its too late.
> > >
> > >
> > >
> > > On Tue, Sep 8, 2015 at 4:05 PM, Ryan G
> > > <ngsbioinformat...@gmail.com  ngsbioinformat...@gmail.com>
> > > <mailto:ngsbioinformat...@gmail.com  ngsbioinformat..

Re: [galaxy-dev] External User Authenticaion

[Ryan G]

We have Apache set up to authenticate users off our LDAP.  If they
authenticate correctly, they are then forwarded on through the proxy.

What I want is to prevent users from hitting the galaxy URL directly.  If
they, do I want to automatically redirect them to the proxy.


On Tue, Oct 13, 2015 at 11:10 AM, Eric Rasche <e...@tamu.edu> wrote:

> Hi Ryan,
>
> On 10/13/2015 09:50 AM, Ryan G wrote:
> > Hi all - In regards to external user authentication that I have working
> > now (see thread below).  When users try to go to the actual Galaxy page,
> > they get the message:
> >
> >
> > Access to Galaxy is denied
>
> That's expected for External User Auth if you don't have the REMOTE_USER
> header set properly.
>
> >
> > Galaxy is configured to authenticate users via an external method (such
> > as HTTP authentication in Apache), but no shared secret key was provided
> > by the upstream (proxy) server.
> >
> > Please contact your local Galaxy administrator. The variable
> > |remote_user_secret| and |GX_SECRET| header must be set before you may
> > access Galaxy.
> >
> >
> >
> > That's fine and all but I'd like to have them redirected to the real
> > login page.  Is there a way to do this?  I didn't see anything obvious
> > and was thinking of adding a parameter to galaxy.ini and have Galaxy
> > automatically forward them after 5 seconds or so.
>
> What external auth mechanism are you using?
>
> >
> > Ryan
> >
> >
> > On Tue, Oct 13, 2015 at 10:49 AM, Ryan G <ngsbioinformat...@gmail.com
> > <mailto:ngsbioinformat...@gmail.com>> wrote:
> >
> > Hi all - In regards to external user authentication that I have
> > working now (see thread below).  When users try to go to the actual
> > Galaxy page, they get the message:
> >
> >
> > On Thu, Oct 1, 2015 at 4:10 PM, Ryan G <ngsbioinformat...@gmail.com
> > <mailto:ngsbioinformat...@gmail.com>> wrote:
> >
> > I finally got around to this and all is working well.  I
> > submitted 2 patches to remoteuser.py to assist in debugging
> > incorrect set ups.
> >
> > Last question - When a user logs out, they get the page ""Access
> > to Galaxy user controls is disabled".  I've set the
> >     remote_user_logout_href parameter to a different website, but
> > they still get the "Access to Galaxy user controls is disabled".
> >
> > I see it in lib/galaxy/webapps/galaxy/controllers/user.py, but I
> > think at that point its too late.
> >
> >
> >
> > On Tue, Sep 8, 2015 at 4:05 PM, Ryan G
> > <ngsbioinformat...@gmail.com
> > <mailto:ngsbioinformat...@gmail.com>> wrote:
> >
> > Yes, I have a test server I'm going to check this one.
> > thanks for the link, that's perfect...I'll add some
> > debugging code in here to see what's going on.
> >
> > On Tue, Sep 8, 2015 at 1:46 PM, Dannon Baker
> > <dannon.ba...@gmail.com <mailto:dannon.ba...@gmail.com>>
> wrote:
> >
> > Do you have a way to verify the "HTTP_MAIL" header is
> > actually being passed through your proxy server?
> >
> > The problem is that Galaxy still doesn't think it's
> > receiving the expected headers, so there isn't a good
> > way that it can tell you more about what might be going
> > on.  If you're able to tweak Galaxy (using a test
> >     server) and add a few logging statements the code, this
> > would be good places to check what's going on (print the
> > `environ` dictionary associated with that request, along
> > with self.remote_user_header to see what Galaxy is
> > actually trying to use):
> >
> >
> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/framework/middleware/remoteuser.py#L49
> >
> > -Dannon
> >
> > On Thu, Sep 3, 2015 at 1:51 PM, Ryan G
> > <ngsbioinformat...@gmail.com
> > <mailto:ngsbioinformat...@gmail.com>> wrote:
> >
> > It turns out our authentication system passes a
> > header 'HTTP_MAIL' which contains the users email
> > address.  

[galaxy-dev] External User Authenticaion

[Ryan G]

Hi all - I'm trying to use external user authentication with Galaxy.  The
external authentication passes to Galaxy the username with the mail domain
at HTTP_USER.

In galaxy.ini, I enable:
use_remote_user = True


When I try to access Galaxy, I get the message:
Galaxy is configured to authenticate users via an external method (such as
HTTP authentication in Apache), but a username was not provided by the
upstream (proxy) server. This is generally due to a misconfiguration in the
upstream server.

But nothing in paster.log indicating what the error is.

How do I track this down?
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Re: [galaxy-dev] External User Authenticaion

[Ryan G]

Yes, I have a test server I'm going to check this one.  thanks for the
link, that's perfect...I'll add some debugging code in here to see what's
going on.

On Tue, Sep 8, 2015 at 1:46 PM, Dannon Baker <dannon.ba...@gmail.com> wrote:

> Do you have a way to verify the "HTTP_MAIL" header is actually being
> passed through your proxy server?
>
> The problem is that Galaxy still doesn't think it's receiving the expected
> headers, so there isn't a good way that it can tell you more about what
> might be going on.  If you're able to tweak Galaxy (using a test server)
> and add a few logging statements the code, this would be good places to
> check what's going on (print the `environ` dictionary associated with that
> request, along with self.remote_user_header to see what Galaxy is actually
> trying to use):
>
>
> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/framework/middleware/remoteuser.py#L49
>
> -Dannon
>
> On Thu, Sep 3, 2015 at 1:51 PM, Ryan G <ngsbioinformat...@gmail.com>
> wrote:
>
>> It turns out our authentication system passes a header 'HTTP_MAIL' which
>> contains the users email address.  In galaxy.ini, I have
>>
>> use_remote_user = True
>> remote_user_header = HTTP_MAIL
>>
>> After restarting,Galaxy still gives the same error.
>>
>> On Mon, Aug 31, 2015 at 3:44 PM, Dannon Baker <dannon.ba...@gmail.com>
>> wrote:
>>
>>> Hi Ryan,
>>>
>>> It may be that Galaxy is looking for a different remote user header than
>>> your proxy is setting.  I believe by default we look for HTTP_REMOTE_USER,
>>> but this is configurable in galaxy.ini (so, you could set yours to
>>> HTTP_USER there).  Let me know if this doesn't sort it out for you and we
>>> can dig deeper!
>>>
>>> -Dannon
>>>
>>> On Mon, Aug 31, 2015 at 3:42 PM, Ryan G <ngsbioinformat...@gmail.com>
>>> wrote:
>>>
>>>> Hi all - I'm trying to use external user authentication with Galaxy.
>>>> The external authentication passes to Galaxy the username with the mail
>>>> domain at HTTP_USER.
>>>>
>>>> In galaxy.ini, I enable:
>>>> use_remote_user = True
>>>>
>>>>
>>>> When I try to access Galaxy, I get the message:
>>>> Galaxy is configured to authenticate users via an external method (such
>>>> as HTTP authentication in Apache), but a username was not provided by the
>>>> upstream (proxy) server. This is generally due to a misconfiguration in the
>>>> upstream server.
>>>>
>>>> But nothing in paster.log indicating what the error is.
>>>>
>>>> How do I track this down?
>>>>
>>>>
>>>>
>>>> ___
>>>> Please keep all replies on the list by using "reply all"
>>>> in your mail client.  To manage your subscriptions to this
>>>> and other Galaxy lists, please use the interface at:
>>>>   https://lists.galaxyproject.org/
>>>>
>>>> To search Galaxy mailing lists use the unified search at:
>>>>   http://galaxyproject.org/search/mailinglists/
>>>>
>>>
>>>
>>
>
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Re: [galaxy-dev] External User Authenticaion

[Ryan G]

I finally got around to this and all is working well.  I submitted 2
patches to remoteuser.py to assist in debugging incorrect set ups.

Last question - When a user logs out, they get the page ""Access to Galaxy
user controls is disabled".  I've set the remote_user_logout_href parameter
to a different website, but they still get the "Access to Galaxy user
controls is disabled".

I see it in lib/galaxy/webapps/galaxy/controllers/user.py, but I think at
that point its too late.



On Tue, Sep 8, 2015 at 4:05 PM, Ryan G <ngsbioinformat...@gmail.com> wrote:

> Yes, I have a test server I'm going to check this one.  thanks for the
> link, that's perfect...I'll add some debugging code in here to see what's
> going on.
>
> On Tue, Sep 8, 2015 at 1:46 PM, Dannon Baker <dannon.ba...@gmail.com>
> wrote:
>
>> Do you have a way to verify the "HTTP_MAIL" header is actually being
>> passed through your proxy server?
>>
>> The problem is that Galaxy still doesn't think it's receiving the
>> expected headers, so there isn't a good way that it can tell you more about
>> what might be going on.  If you're able to tweak Galaxy (using a test
>> server) and add a few logging statements the code, this would be good
>> places to check what's going on (print the `environ` dictionary associated
>> with that request, along with self.remote_user_header to see what Galaxy is
>> actually trying to use):
>>
>>
>> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/framework/middleware/remoteuser.py#L49
>>
>> -Dannon
>>
>> On Thu, Sep 3, 2015 at 1:51 PM, Ryan G <ngsbioinformat...@gmail.com>
>> wrote:
>>
>>> It turns out our authentication system passes a header 'HTTP_MAIL' which
>>> contains the users email address.  In galaxy.ini, I have
>>>
>>> use_remote_user = True
>>> remote_user_header = HTTP_MAIL
>>>
>>> After restarting,Galaxy still gives the same error.
>>>
>>> On Mon, Aug 31, 2015 at 3:44 PM, Dannon Baker <dannon.ba...@gmail.com>
>>> wrote:
>>>
>>>> Hi Ryan,
>>>>
>>>> It may be that Galaxy is looking for a different remote user header
>>>> than your proxy is setting.  I believe by default we look for
>>>> HTTP_REMOTE_USER, but this is configurable in galaxy.ini (so, you could set
>>>> yours to HTTP_USER there).  Let me know if this doesn't sort it out for you
>>>> and we can dig deeper!
>>>>
>>>> -Dannon
>>>>
>>>> On Mon, Aug 31, 2015 at 3:42 PM, Ryan G <ngsbioinformat...@gmail.com>
>>>> wrote:
>>>>
>>>>> Hi all - I'm trying to use external user authentication with Galaxy.
>>>>> The external authentication passes to Galaxy the username with the mail
>>>>> domain at HTTP_USER.
>>>>>
>>>>> In galaxy.ini, I enable:
>>>>> use_remote_user = True
>>>>>
>>>>>
>>>>> When I try to access Galaxy, I get the message:
>>>>> Galaxy is configured to authenticate users via an external method
>>>>> (such as HTTP authentication in Apache), but a username was not provided 
>>>>> by
>>>>> the upstream (proxy) server. This is generally due to a misconfiguration 
>>>>> in
>>>>> the upstream server.
>>>>>
>>>>> But nothing in paster.log indicating what the error is.
>>>>>
>>>>> How do I track this down?
>>>>>
>>>>>
>>>>>
>>>>> ___
>>>>> Please keep all replies on the list by using "reply all"
>>>>> in your mail client.  To manage your subscriptions to this
>>>>> and other Galaxy lists, please use the interface at:
>>>>>   https://lists.galaxyproject.org/
>>>>>
>>>>> To search Galaxy mailing lists use the unified search at:
>>>>>   http://galaxyproject.org/search/mailinglists/
>>>>>
>>>>
>>>>
>>>
>>
>
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[galaxy-dev] External Pipeline Cleanup

[Ryan G]

Hi all - For various reasons, we've had to implement our pipelines external
to Galaxy, but still give Galaxy the ability to run them.  I've
accomplished this by having the Galaxy tool wrapper call the external app
to launch the pipelines.

My problem is that when a user aborts the tool, the tool needs to be able
to communicate to the pipeline that its need aborted.  How can I do this?
Is there some way to get a notification that the job has been cancelled
before its actually cancelled to perform clean up?
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Re: [galaxy-dev] tabular file displayed without tabs

[Ryan G]

The format is listed as tabular when I view details.

In fact, in the preview window in the History Pane, it recognizes there are
columns and that the data is in fact tabular, but when displaying, this
isn't the case.



On Tue, May 24, 2016 at 4:20 PM, Carl Eberhard <carlfeberh...@gmail.com>
wrote:

> Ok - if it's not zebra striped and it's word wrapping, then it's somehow
> not displaying as tabular - you're correct.
>
> If you click on the 'View details' button of that dataset (the 'i' with
> the circle around it shown when the dataset is expanded in the right hand
> side of the 'Analyze Data' page), what does it list the 'Format' as?
> 'tabular'? (This is also listed as 'Format' in the expanded view itself).
>
> On Mon, May 23, 2016 at 5:33 PM, Ryan G <ngsbioinformat...@gmail.com>
> wrote:
>
>> Odd because I have another tabular file that is displayed with every
>> other line highlighted and there is not word-wrapping on the file.  However
>> the file that has the type tabular and displayed as text is word-wrapped
>> with no lines highlighted.  I suspect its not actually recognized as
>> tabular or is being overridden where.
>>
>>
>> On Thu, Nov 12, 2015 at 10:23 AM, Carl Eberhard <carlfeberh...@gmail.com>
>> wrote:
>>
>>> Hi, Ryan
>>>
>>> Galaxy displays tabular data in the browser using a  tag. It
>>> *sounds like* the behavior you see (columns losing space between one
>>> another when narrowing the window and getting more space as you expand the
>>> window) would reflect that.
>>>
>>> Carl
>>>
>>> On Wed, Oct 28, 2015 at 1:23 PM, Ryan G <ngsbioinformat...@gmail.com>
>>> wrote:
>>>
>>>> The file is an output from a tool and in the tool's xml, its format is
>>>> tabular.
>>>>
>>>>
>>>>
>>>> On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning <
>>>> bjoern.gruen...@gmail.com> wrote:
>>>>
>>>>> Hi Ryan,
>>>>>
>>>>> is it recognised as 'tabular'?
>>>>>
>>>>> Ciao,
>>>>> Bjoern
>>>>>
>>>>> Am 27.10.2015 um 04:42 schrieb Ryan G:
>>>>> > Hi - I have a tools that generates a tab-delimited text file as
>>>>> output.
>>>>> > when I click the eye icon to view the data, all the fields are
>>>>> compressed
>>>>> > as if there were no tabs.  If I expand the history view, the little
>>>>> preview
>>>>> > window shows the contents as tabbed.  I've verified that the spaces
>>>>> are
>>>>> > indeed '\t' tab characters.  Why would Galaxy not display this file
>>>>> as a
>>>>> > tab-delimited file?
>>>>> >
>>>>> >
>>>>> >
>>>>> > ___
>>>>> > Please keep all replies on the list by using "reply all"
>>>>> > in your mail client.  To manage your subscriptions to this
>>>>> > and other Galaxy lists, please use the interface at:
>>>>> >   https://lists.galaxyproject.org/
>>>>> >
>>>>> > To search Galaxy mailing lists use the unified search at:
>>>>> >   http://galaxyproject.org/search/mailinglists/
>>>>> >
>>>>>
>>>>
>>>>
>>>> ___
>>>> Please keep all replies on the list by using "reply all"
>>>> in your mail client.  To manage your subscriptions to this
>>>> and other Galaxy lists, please use the interface at:
>>>>   https://lists.galaxyproject.org/
>>>>
>>>> To search Galaxy mailing lists use the unified search at:
>>>>   http://galaxyproject.org/search/mailinglists/
>>>>
>>>
>>>
>>
>
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Re: [galaxy-dev] Login reguried causing nested main page loading

[Ryan G]

I've seen this as well.  I find that restarting galaxy fixes the problem but 
I'd love to know the underlying cause.  

Please excuse any typos -- Sent from my iPhone

> On Jan 11, 2016, at 5:08 AM, Christian Brenninkmeijer 
>  wrote:
> 
> Hi All,
> 
> I tried to turn on login required in config.ini
> 
> But now if you are not logged in it loads the main page where normally the 
> welcome.html would go.
> Which then recursively loads other main pages.
> 
> Which file am I missing?
> 
> Thanks
> Christian
> University of Manchester
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[galaxy-dev] Restricting tool input to 1 dataset instead of multiple

[Ryan G]

Hi all - I'm creating a tool in Galaxy that takes as input several datasets
for different variables.  For each variable, I want to restrict the input
to a single dataset.  The docs,
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax, indicate
type="data" needs to be set for a dataset from the current history to be
available for input.  When I do this, Galaxy displays the icon for Single
Dataset, Mulitple Datasets, and Dataset collection.

I only want to give the option for Single Dataset.  I tried include
multiple="false", but that doesn't seem to have any effect.  Is there a way
to accomplish this?
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[galaxy-dev] Custom tool with multiple inputs for different datasets. How to preferrentially select

[Ryan G]

Next question - My custom tool take as input mulitple datasets from
different tools and collates all the information.  For instance, 1 input as
tabular input, sampleManifest, another input is also tabular,
expressionData.

When the tool is display, both entries default to the most recent tabular
dataset in the history.  Is there a way to have Galaxy try to guess which
dataset to default to as input instead of always choosing the latest input
for all the fields?
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[galaxy-dev] Cloudman & AWS IAM_PROFILE support?

[Ryan G]

Hi - Does Cloudman support IAM_PROFILES?   We run our instances within a
VPC and assign an IAM_PROFILE to the ec2 instances so that they have access
to resouces.   Does Cloudman have this support?
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Re: [galaxy-dev] Cloudman & AWS IAM_PROFILE support?

[Ryan G]

We actually have galaxy running within a VPC now. The problem we're running 
into is that when ec2 instances get created they don't have an I_am profile 
attached to them so they can't get access to S3 resources. This should just be 
a parameter past to AWS when the instances get created to attach the Iam 
profile. I just need to know where the code for creating ec2 instances is and I 
can test it out. 

Please excuse any typos -- Sent from my iPhone

> On Mar 15, 2016, at 10:46 PM, Chris Dagdigian  wrote:
> 
> 
> Hi Ryan,
> 
> I've never been able to get cloudman to function within a private VPC so if 
> this is your architecture as well and you manage to make progress I'd be 
> interested in learning your methods. Thanks!
> 
> Regards,
> Chris
> 
> 
> Enis Afgan wrote:
>> Hi Ryan,
>> I'm not sure I really understand your question but CloudMan can run under an 
>> IAM account - it is just necessary to give the IAM user permissions to 
>> create EC2 and S3 resources. Let us know if that's not what you had in mind 
>> or if you have any more questions.
>> 
>> Cheers,
>> Enis
> 
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Re: [galaxy-dev] Python 2.7 vs 2.6 for galaxy after 16.01

[Ryan G]

We Iocally compile 2.7.8 and keep it in a distinct location that our paths 
references. 

This is very easy and has worked well for us. 

Please excuse any typos -- Sent from my iPhone

> On Mar 21, 2016, at 5:32 PM, Peter Cock  wrote:
> 
> Hi D. K.,
> 
> We're currently trying a locally compiled Python 2.7 (from source)
> under the shared Galaxy mount for use with a CentOS 6 cluster
> and Galaxy server.
> 
> This seems to be working once we got the $PATH working for
> cluster jobs (initially they would try to set the Galaxy metadata
> using the system Python 2.6, which would fail).
> 
> I don't know if this is any easier than using the CenOS Software
> Collections as suggested by Nicola, especially when it comes to
> updating the OS.
> 
> Peter
> 
>> On Mon, Mar 21, 2016 at 5:59 PM, Nicola Soranzo  wrote:
>> Hi Daniel,
>> I've been using python27 from CentOS Software Collections for quite some
>> time. It's a bit annoying because you have to remember to load it, but it is
>> surely doable.
>> 
>> Cheers,
>> Nicola
>> 
>> 
>> On 21/03/16 17:46, D K wrote:
>> 
>> Hi Galaxy Devs,
>> 
>> This may be premature but I read that for Galaxy after 16.01 that the plan
>> is for python 2.6 to no longer be supported. I'm currently running CentOS
>> 6.6 which uses python 2.6. In order to be able to use newer versions of
>> Galaxy is my only option to upgrade to a newer version of CentOS? Is it
>> possible to use Conda, RedHat Software Collections or some other similar
>> method instead of doing this upgrade?
>> 
>> Thanks!
>> 
>> 
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Re: [galaxy-dev] Galaxy 15.10 Jobs not running

[Ryan G]

Hi Nate - Thanks.  Our galaxy.ini shows:

job_config_file = config/job_conf.xml

Our job_conf.xml is (which is the same as job_conf.xml.sample_basic) :














Hmmm, ok weird.  We just restart Galaxy for the 5th or 6th time to get a
clean log file to send and it works now.   Hmmm.   I will consider this
issue closed.   Is there any documention that talks about how the job
runner and manager, all work together?  I'd like to add some debugging
statements in the code so there is more info in the log file.



On Wed, Mar 2, 2016 at 12:00 PM, Nate Coraor <n...@bx.psu.edu> wrote:

> On Tue, Mar 1, 2016 at 1:19 PM, Ryan G <ngsbioinformat...@gmail.com>
> wrote:
>
>> Hi all - We recently merged in Galaxy 15.10 changes into our staging
>> instance and have noticed jobs are no longer dispatched.  There is no
>> obvious problem in the log file.
>>
>> I see in github, commits have recently been made to revert something, but
>> I'm not clear what.
>>
>> Is there something going on with the job runner?  Better yet, how can I
>> track down what my issue is?
>>
>
> Hi Ryan,
>
> There aren't any current issues with job running that I'm aware of.
> Typically the first thing to check is your job_conf.xml and make sure that
> handlers defined are the same as handlers (with matching server names) that
> you are starting). The log for your handlers should show them loading the
> job_conf.xml and setting up job plugins if they are identified as handlers
> in the config.
>
> --nate
>
>
>>
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[galaxy-dev] possible bug found - unable to log out of impersonated user when external authentication enabled

[Ryan G]

Hi all - We are using a SSO system so that user's authenticate externally
from Galaxy.

when I impersonate a user then try to log out as that user, I'm unable to.
I get the page "
Access to Galaxy user controls is disabled

User controls are disabled when Galaxy is configured for external
authentication."


If I close the browser down, and restart, I get my SSO log in page, but
when I get to Galaxy, I'm still impersonating the user.
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Re: [galaxy-dev] possible bug found - unable to log out of impersonated user when external authentication enabled

[Ryan G]

Thanks.  Clearing out the browser history resolved it but there should be a
better way...

On Wed, Jul 27, 2016 at 12:48 PM, Dannon Baker <dannon.ba...@gmail.com>
wrote:

> Hey, thanks for this.  I've made an issue (
> https://github.com/galaxyproject/galaxy/issues/2671)  and will check it
> out today.
>
> On Wed, Jul 27, 2016 at 12:44 PM Ryan G <ngsbioinformat...@gmail.com>
> wrote:
>
>> Hi all - We are using a SSO system so that user's authenticate externally
>> from Galaxy.
>>
>> when I impersonate a user then try to log out as that user, I'm unable
>> to.  I get the page "
>> Access to Galaxy user controls is disabled
>>
>> User controls are disabled when Galaxy is configured for external
>> authentication."
>>
>>
>> If I close the browser down, and restart, I get my SSO log in page, but
>> when I get to Galaxy, I'm still impersonating the user.
>>
>>
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>
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[galaxy-dev] Removing job in error state

[Ryan G]

Hi - In the Manage Jobs admin job, I have a job from a user that never ran
successfully.   It shows:
Job ID User Last Update Tool State Inputs Command Line Job Runner PID/Cluster
ID
12772 u...@company.com 654 hours ago cshl_fastx_collapser new 13653 error
None None None
How do I remove this job?  I can't find a way to delete it.
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Re: [galaxy-dev] Removing job in error state

[Ryan G]

Thanks.   That fixed it.

On Thu, Aug 4, 2016 at 3:19 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:

> Hi Ryan
>
> If the "Stop Jobs" option on the Admin page does not work, you can go for
> the direct way by manually interacting with the PostgreSQL database:
>
> Change the state to "error"  in the 'job' table, eg:
>
> update job set state='error' where id=12772;
>
>
> As always, be very careful when you directly access the PostgreSQL
> database! Make sure your database is properly backed up. And you should
> only consider this as the very last option.
>
>
> Hans-Rudolf
>
>
> On 08/04/2016 06:02 AM, Ryan G wrote:
>
>> Hi - In the Manage Jobs admin job, I have a job from a user that never
>> ran successfully.   It shows:
>> Job ID  UserLast Update ToolState   Inputs  Command Line
>> Job Runner
>> PID/Cluster ID
>> 12772   u...@company.com <mailto:u...@company.com>  654
>> hours ago
>> cshl_fastx_collapsernew 13653 error NoneNoneNone
>>
>>
>> How do I remove this job?  I can't find a way to delete it.
>>
>>
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>>
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Re: [galaxy-dev] provide a field to upload a file as part of tool input

[Ryan G]

I figured out the optional part (RTFM to myself)




On Fri, Aug 5, 2016 at 6:54 PM, Ryan G <ngsbioinformat...@gmail.com> wrote:

> Hi all - I have a custom tool that can optionally take a file as input.
>
> Right now, users have to upload the file into their history, then select
> the file when running the tool.
>
> Is there a way to let the user select a file local on their computer as
> input to the tool, then when run, the file is uploaded?
>
> And (second question), how can I make this field optional, such that the
> user does not need to provide a file at all when running the tool?
>
> Right now, my input field is:
>
> 
>
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[galaxy-dev] provide a field to upload a file as part of tool input

[Ryan G]

Hi all - I have a custom tool that can optionally take a file as input.

Right now, users have to upload the file into their history, then select
the file when running the tool.

Is there a way to let the user select a file local on their computer as
input to the tool, then when run, the file is uploaded?

And (second question), how can I make this field optional, such that the
user does not need to provide a file at all when running the tool?

Right now, my input field is:


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Re: [galaxy-dev] Development/production instances updates management

[Ryan G]

We do exactly this.

We have a staging instance, and a production instance.   Both exist in a
single git repo as separate branches.  The main different for this is that
the staging and production config file point to different port and database
instances.

We also maintain a staging and production python environment to match.

Changes always flow from staging to production and follow the git branch
modeling from http://nvie.com/posts/a-successful-git-branching-model/

This has worked EXTREMELY well for us.



On Wed, Aug 31, 2016 at 3:00 AM, Mathieu Bahin <
mathieu.ba...@biologie.ens.fr> wrote:

> Hi all,
>
> First of all, I'm new to this list and already posted my question on
> biostar. Thanks to Hans-Rudolf for his answer but I'm not sure we have
> exactly the same constraints here and I send this message to try to get
> other answers and see what is the best solution for us.
>
> I'm trying to setup a good galaxy environment for a biology institute.
> To do so, I need to have a development and a production instances that
> are clones on the structure side. I'd like to update regularly these
> instances (following more or less galaxy main updates) and track them
> with git repos.
>
> I'm pretty sure lot of galaxy admins are trying to do that but I can't
> find the answer.
>
> My idea was to have a local git repo to save the development instance
> (not the data). When there is a new update, I git pull it from galaxy
> GitHub, compare what changed in the sample files and make the
> appropriate changes in the config files corresponding to these samples.
> Then I would git push towards the production instance. To do so, I need
> to have a proper .gitignore file (listing especially the data files). I
> saw that there is a .gitignore in the galaxy GitHub repo. It's probably
> relevant when I want to pull the updates but I'm not sure it is
> regarding the transfers between the development and production instances
> (for example, the config files have to be tracked I guess).
>
> Cheers,
> Mathieu
>
> --
> 
> ---
> | Mathieu Bahin
> | IE CNRS
> |
> | Institut de Biologie de l'Ecole Normale Supérieure (IBENS)
> | Biocomp team
> | 46 rue d'Ulm
> | 75230 PARIS CEDEX 05
> | 01.44.32.23.56
> 
> ---
>
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Re: [galaxy-dev] Converting an internal user to an external user

[Ryan G]

Sorry, missed your other questions...

external authentication via apache...yes.  Its working well for us.
The userid is the same.  I'm clearly missing something.   I need to find in
the code where this is and add some debugging statements.

On Wed, Sep 7, 2016 at 12:15 PM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:

> Hi Ryan
>
> Are you doing external authentication via apache?
>
> if so, I suggest to change the value in the 'external' column from 'f' to
> 't' in the galaxy_user table.
>
> also, check, whether the e-mail used is really the same as the one coming
> from your external authentication system.
>
> However, be very careful, whenever you manually interact with the Galaxy
> PostgreSQL database. Make sure you have an up-to-date back-up.
>
> Hope this helps,
> Hans-Rudolf
>
>
>
>
> On 09/07/2016 05:27 PM, Ryan G wrote:
>
>> Hi all - I'm having a problem with a user account and Galaxy getting
>> confused with it being internal vs external.
>>
>> When we first set up galaxy, we were using Galaxy's internal
>> authentication system.  This worked well but all our users then had
>> another password to keep track of.
>>
>> We activated external user authentication a few months ago and it works
>> fine for us.
>>
>> This user hasn't logged in since and recently tried but is unable to.
>>
>> I discovered her account in Galaxy appears as an internal account eg
>> created before we were using external authentication.   Now that we have
>> external authentication, Galaxy doesn't recognize her and she gets the
>> user_disabled page whenever she tries to log in.
>>
>> Is there a way I can change her account in Galaxy from being an internal
>> to an external account?
>>
>> Ryan
>>
>>
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Re: [galaxy-dev] Converting an internal user to an external user

[Ryan G]

Ok I got it.  I had to update the email address field to match what the
REMOTE_USER variable was being set my Apache.

On Wed, Sep 7, 2016 at 1:41 PM, Ryan G <ngsbioinformat...@gmail.com> wrote:

> Sorry, missed your other questions...
>
> external authentication via apache...yes.  Its working well for us.
> The userid is the same.  I'm clearly missing something.   I need to find
> in the code where this is and add some debugging statements.
>
> On Wed, Sep 7, 2016 at 12:15 PM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
>
>> Hi Ryan
>>
>> Are you doing external authentication via apache?
>>
>> if so, I suggest to change the value in the 'external' column from 'f' to
>> 't' in the galaxy_user table.
>>
>> also, check, whether the e-mail used is really the same as the one coming
>> from your external authentication system.
>>
>> However, be very careful, whenever you manually interact with the Galaxy
>> PostgreSQL database. Make sure you have an up-to-date back-up.
>>
>> Hope this helps,
>> Hans-Rudolf
>>
>>
>>
>>
>> On 09/07/2016 05:27 PM, Ryan G wrote:
>>
>>> Hi all - I'm having a problem with a user account and Galaxy getting
>>> confused with it being internal vs external.
>>>
>>> When we first set up galaxy, we were using Galaxy's internal
>>> authentication system.  This worked well but all our users then had
>>> another password to keep track of.
>>>
>>> We activated external user authentication a few months ago and it works
>>> fine for us.
>>>
>>> This user hasn't logged in since and recently tried but is unable to.
>>>
>>> I discovered her account in Galaxy appears as an internal account eg
>>> created before we were using external authentication.   Now that we have
>>> external authentication, Galaxy doesn't recognize her and she gets the
>>> user_disabled page whenever she tries to log in.
>>>
>>> Is there a way I can change her account in Galaxy from being an internal
>>> to an external account?
>>>
>>> Ryan
>>>
>>>
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>>>
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>>>http://galaxyproject.org/search/mailinglists/
>>>
>>>
>
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[galaxy-dev] Elastic Bean Stalk

[Ryan G]

Hi all - I was wondering, if we deploy Galaxy in AWS, can we take advantage
of Elastic BeanStalk to scale our instances based on demand instead of
trying to configure Galaxy to perform well for our users?

Ryan
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