Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

[Christian Brenninkmeijer]

To follow up on what Peter says

It is the code in 
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py
from line 182
class Bam( Binary ):

This code (set_meta) is called after the tool has finished running while it is 
copying the resulting data into the galaxy database.
If the bam file is unsorted or incorrectly sorted any tool fails.

But if the _get_samtools_version methods found the early version of samtools it 
crashed our galaxy.

2 issues here.
1. Galaxy will only handle sorted bam files (regrettable but that is political)
2. While galaxy has wheels (previously eggs) for all other dependencies it 
relies on locally installed samtools.  Can this really not be fixed???

Christian
University of Manchester



From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Peter Briggs [peter.bri...@manchester.ac.uk]
Sent: Tuesday, May 24, 2016 12:04 PM
To: Raymond Wan
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

Hello Ray

Just to clarify, for us it wasn't dependent on the tool - it was
actually the version of samtools installed in the 'galaxy' user's
environment i.e. on the 'galaxy' user's PATH.

I set it explicitly by creating a file called "local_env.sh" in the
'config' directory of the Galaxy installation with the following content:

$ cat local_env.sh
# Prepend samtools 1.2
export PATH=$HOME/apps/samtools/1.2/bin:$PATH
##
#

which is automatically picked up by 'run.sh' when Galaxy is started (I
don't know how that plays if you're using a uwsgi/supervisor setup).

Best wishes

Peter

On 24/05/16 11:46, Raymond Wan wrote:
> Hi Peter,
>
>
> On Tue, May 24, 2016 at 6:29 PM, Peter Briggs
>  wrote:
>> One of my colleagues encountered a similar-sounding error on our local test
>> instance, where an unsorted BAM file seemed to crash the Galaxy handler
>> processes and prevented them from restarting.
>>
>> In our case the default samtools version in the Galaxy environment was
>> 0.1.18; we found that updating this to samtools 1.2 fixed the crash problem.
>
>
> Ah!  That does sound familiar.  As I just replied in another message,
> we seem to have at least 5 versions of samtools in the system.  I'm
> not sure if that is normal or not for a Galaxy instance...
>
> Let me see if I can figure out (through logs, but most likely by
> asking the user) what tool he was using and figure out which samtools
> executable was being run.  If it is 0.1.18, I'll look into update
> it...thank you for sharing your colleague's experience!
>
> Ray
>

--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Re: [galaxy-dev] Kallisto tool wrapper?

[Christian Brenninkmeijer]

Have a look at:
https://github.com/galaxyproject/galaxy/blob/master/lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py

This will attempt to find any dependencies previously install from a toolshed 
to use in Planemo.

Christian

PS.
If your package is not exactly named you may have to comment out the condition
if package_name.lower().startswith("package_" + name.lower()):




From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Langhorst, Brad [langho...@neb.com]
Sent: Friday, April 29, 2016 5:30 PM
To: Anthony Bretaudeau
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Kallisto tool wrapper?

Salmon works in a similar way to kallisto.
I’ve been tweaking the test toolshed wrapper of that lately, but I have not yet 
figured out how to get planemo to test it properly - as soon as I do i’ll 
publish it to the toolshed.


Brad
—
Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs




On Apr 29, 2016, at 11:07 AM, Anthony Bretaudeau 
> wrote:

Hi,

While working on Trinity, I made a package (but no wrapper) for it in IUC: 
https://github.com/galaxyproject/tools-iuc/pull/613

It is not yet merged because of a licence problem though...


On 29/04/2016 16:37, Lance Parsons wrote:
I've had requests from users to install Kallisto as Galaxy tool. I didn't see 
any wrappers or evidence of wrappers in my searching, but I thought I'd ask 
here to see if anyone is working on or interested in working on such a thing.


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[galaxy-dev] tool shed bug on uploading incorrect files

[Christian Brenninkmeijer]

Hi All,

There is a bug in the toolshed code when you upload a file with an error.

For example a jar file containing an tool_dependency.xml which refers to a non 
existing dependency.

The toolshed correct refuses to except the upload and stays at the old version,

However the files are added to the database/community_files/xxx/repo_yyy 
directory.

If I then later upload a different jar with different files the previous files 
are NOT deleted.

If you try to delete there from the webbrouser you get an error.

Quick Fix is to go into database/community_files/xxx/repo_yyy and delete the 
files manually.

Christian
University of Manchester

PS. I was able to replicate this with a brand new toolshed.

create admin user, category ect

create a tool and add a jar with a tool_dependecy.xml file with which reference 
a dependency not there

upload a different jar which does not include a tool_dependency.xml file

browse ...tip file

mark tool_dependency.xml which is showing and attempt to delete.


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Re: [galaxy-dev] Troubleshooting BAM file upload issues

[Christian Brenninkmeijer]

Try using samtools to sort the BAM before uploading.

samtools sort original.bam  sorted.bam

This will help with two things.

1. Check the original file is not corrupt

2. Put the BAM in the only order galaxy will accept.

Christian
University of Manchester

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Amelia Ireland [airel...@lbl.gov]
Sent: Wednesday, March 23, 2016 8:24 PM
To: Daniel Blankenberg
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Troubleshooting BAM file upload issues

I'm using the standard 'Upload file' tool, and choosing some local files. I can 
successfully upload these files to the galaxy installation on my laptop and to 
the usegalaxy.org server, but uploading them to the 
galaxy installation on the server results in their appearing to be empty and 
the error message about uploaded file containing inappropriate content.

I'm not sure where to proceed from here. Some things I'd like to explore, but 
am not sure how to do so in Galaxy world, are:

- check that the file has uploaded properly
- manually run the tool script on the input file to ensure there's not some 
error that I'm missing




On 23 March 2016 at 12:53, Daniel Blankenberg 
> wrote:
Hi Amelia,

How are you uploading the files?

If you are using a copy and pasted URL, can you make sure that the example file 
exists and is accessible to the machine where the Galaxy job is running.

A 404 error, for example, can often masquerade as a “The uploaded file contains 
inappropriate HTML content” error (although this shouldn’t be the outcome of 
this tool, it should be a red dataset stating a 404 error, in this case).



Thanks for using Galaxy,

Dan




On Mar 23, 2016, at 3:30 PM, Amelia Ireland 
> wrote:

On 23 March 2016 at 01:00, Björn Grüning 
> wrote:
Hi Amelia,

can you pleae check if you have samtools installed in your PATH?

I've got it in my tool dependencies dir and it's also available as an 
Environment module.

The tools dependencies file looks like this:



  
  
  
  
  


Debug messages when the tool runs:

galaxy.tools.deps DEBUG 2016-03-23 12:23:05,556 Building dependency shell 
command for dependency 'samtools'
galaxy.tools.deps DEBUG 2016-03-23 12:23:05,556 Find dependency samtools 
version None
galaxy.tools.deps DEBUG 2016-03-23 12:23:05,556 Resolver tool_shed_packages 
returned  
(isnull? True)
galaxy.tools.deps DEBUG 2016-03-23 12:23:05,556 Resolver galaxy_packages 
returned  
(isnull? True)
galaxy.tools.deps DEBUG 2016-03-23 12:23:05,556 Resolver galaxy_packages 
returned  
(isnull? True)
galaxy.tools.deps DEBUG 2016-03-23 12:23:05,556 Resolver modules returned 
 
(isnull? False)
galaxy.jobs.runners DEBUG 2016-03-23 12:23:05,567 (217) command is: 
/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/tool_script.sh;
 return_code=$?; 
MODULEPATH=/usr/share/Modules:/usr/share/Modules/modulefiles:/etc/modulefiles:/usr/common/usg/Modules/modulefiles:/usr/syscom/nsg/modulefiles:/usr/common/jgi/Modules/modulefiles;
 export MODULEPATH; eval `/usr/bin/modulecmd sh load samtools`; python 
"/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/set_metadata_NFVQiC.py"
 "/global/homes/a/aireland/galaxy/database/tmp/tmp5vpBro" 
"/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/galaxy.json"
 
"/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/metadata_in_HistoryDatasetAssociation_349_ZqiKgT,/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/metadata_kwds_HistoryDatasetAssociation_349_CH5HZd,/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/metadata_out_HistoryDatasetAssociation_349_Hb4hhP,/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/metadata_results_HistoryDatasetAssociation_349_2e3dj6,/global/homes/a/aireland/galaxy/database/files/000/dataset_320.dat,/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/metadata_override_HistoryDatasetAssociation_349_pEc2Gh"
 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.local DEBUG 2016-03-23 12:23:05,583 (217) executing job 
script: 
/global/homes/a/aireland/galaxy/database/job_working_directory/000/217/galaxy_217.sh
galaxy.jobs DEBUG 2016-03-23 12:23:05,599 (217) Persisting 
job destination (destination id: local:///)
galaxy.jobs.runners.local DEBUG 2016-03-23 12:23:05,799 execution finished: 
/global/homes/a/aireland/galaxy/database/job_working_directory/000/216/galaxy_216.sh


Am 22.03.2016 um 19:28 schrieb Amelia Ireland:
> I'm setting up a Galaxy instance on a new server and am having some
> issues with BAM file uploads. I'm using the BAM files supplied with
> JBrowse for testing purposes. I have Galaxy installed on my laptop and
> file uploads are 

Re: [galaxy-dev] Troubleshooting BAM file upload issues

[Christian Brenninkmeijer]

The bam support is regrettably different to most of Galaxy.

For some reason it can not make use of Wheels installed by Galaxy but has to 
use native samtools.
Giving very confusing error messages such as file not found if samtools is not 
there.

Also your bam files MUST be sorted by coordinates as BAM sorted by name is not 
a format supported by Galaxy.
For those few tools that expect Bam sorted by name you have to sort inside that 
tool.

Which breaks:
https://toolshed.g2.bx.psu.edu/view/iuc/samtools_sort/38ea74bd4054
As it returns a bam file no longer(or never) supported by Galaxy

I have wasted a number of days on these confusing behaviours.

Christian
University of Manchester


From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Wednesday, March 23, 2016 8:00 AM
To: Amelia Ireland; galaxy-dev@u coordinateslists.galaxyproject.org
Subject: Re: [galaxy-dev] Troubleshooting BAM file upload issues

Hi Amelia,

can you pleae check if you have samtools installed in your PATH?

Ciao,
Bjoern

Am 22.03.2016 um 19:28 schrieb Amelia Ireland:
> I'm setting up a Galaxy instance on a new server and am having some
> issues with BAM file uploads. I'm using the BAM files supplied with
> JBrowse for testing purposes. I have Galaxy installed on my laptop and
> file uploads are working fine, so it's evidently an issue with the
> server and/or OS configuration.
>
> Attempting to upload a BAM file returns the message
>
> "The uploaded binary file contains inappropriate content"
>
> and the upload is empty.
>
> The server is running Scientific Linux and uses the Environment Modules
> system for dependency management. I can successfully upload bed and
> bigwig files, which suggests that samtools is being loaded and
> functioning correctly.
>
> If someone can suggest some troubleshooting steps, I would be most grateful.
>
> Thanks!
> Amelia
>
> Integrated Microbial Genomics (IMG)
> JGI / LBL
>
>
>
> ___
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Re: [galaxy-dev] Difficulty uploading BAM files

[Christian Brenninkmeijer]

It is a shame and a but surprising that unlike most other dependencies samtools 
can not come from an egg now wheel.

Christian

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Marius van den Beek [m.vandenb...@gmail.com]
Sent: Friday, February 26, 2016 6:01 PM
To: Scott Szakonyi
Cc: Galaxy Dev Mailing List
Subject: Re: [galaxy-dev] Difficulty uploading BAM files

Hello Scott,

you do need a samtools binary on GALAXY's PATH.
This is not samtools installed from the toolshed.

Best,
Marius

On 26 February 2016 at 18:49, Scott Szakonyi 
> wrote:
Hi,

I'm having trouble uploading BAM files in our development environment. Other 
files types are uploading without issue. I'm testing with a small BAM file I 
downloaded, and I'm able to successfully upload it on our production server and 
usegalaxy.org. When I try to upload in the development 
environment, I get the following error:

Traceback (most recent call last):
  File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 431, 
in 
__main__()
  File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 420, 
in __main__
add_file( dataset, registry, json_file, output_path )
  File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 347, 
in add_file
if link_data_only == 'copy_files' and 
datatype.dataset_content_needs_grooming( output_path ):
  File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 
218, in dataset_content_needs_grooming
version = self._get_samtools_version()
  File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 
179, in _get_samtools_version
raise Exception(message)
Exception: Attempting to use functionality requiring samtools, but it cannot be 
located on Galaxy's PATH.

I've checked my installed tools, and all the same Samtools packages are 
successfully installed on the development environment as in production. I don't 
see any missing dependencies or anything like that. At this point I'm stumped. 
If anyone can offer some guidance on how to resolve this, I'd be most 
appreciative.

Best regards,

--
Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu

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Re: [galaxy-dev] Difficulty uploading BAM files

[Christian Brenninkmeijer]

I too had trouble with BAM files as

https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py 
Line 201
class Bam( Binary ):
...
def _get_samtools_version( self ):
...
samtools_exec = which('samtools')

Assumes samtools is installed on the server and was not fining one.

I had to install samtools outside of galaxy to get past that.

Christian
University of Manchester

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Scott Szakonyi [scott.b.szakony...@nd.edu]
Sent: Friday, February 26, 2016 5:49 PM
To: Galaxy Dev Mailing List
Subject: [galaxy-dev] Difficulty uploading BAM files

Hi,

I'm having trouble uploading BAM files in our development environment. Other 
files types are uploading without issue. I'm testing with a small BAM file I 
downloaded, and I'm able to successfully upload it on our production server and 
usegalaxy.org. When I try to upload in the development 
environment, I get the following error:

Traceback (most recent call last):
  File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 431, 
in 
__main__()
  File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 420, 
in __main__
add_file( dataset, registry, json_file, output_path )
  File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 347, 
in add_file
if link_data_only == 'copy_files' and 
datatype.dataset_content_needs_grooming( output_path ):
  File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 
218, in dataset_content_needs_grooming
version = self._get_samtools_version()
  File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 
179, in _get_samtools_version
raise Exception(message)
Exception: Attempting to use functionality requiring samtools, but it cannot be 
located on Galaxy's PATH.

I've checked my installed tools, and all the same Samtools packages are 
successfully installed on the development environment as in production. I don't 
see any missing dependencies or anything like that. At this point I'm stumped. 
If anyone can offer some guidance on how to resolve this, I'd be most 
appreciative.

Best regards,

--
Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
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[galaxy-dev] samtools view tools

[Christian Brenninkmeijer]

Hi All,

Has anyone written galaxy tools for the samtools view functions such as

samtools view -f 0x0002 -F 0x0100 -uo

and/or

samtools view -uSo

Thanks
Christian
University of Manchester
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[galaxy-dev] Login reguried causing nested main page loading

[Christian Brenninkmeijer]

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] tools to reduce list of datasets.

[Christian Brenninkmeijer]

Hi All,

Can someone point me to documentations/ examples of how to write a tool to 
reduce a a list of datasets back into a single dataset.

==

What I want to do is process multiple pairs of reads.

1. load all the fastq files.

2. create a list of pairs

3. Run tools of each pair in the list (As a seperate job for each pair)

4. Run a single tool over all the results of 3 at the same time! (One job which 
takes all the files/ whole collection) as input.

thanks in advance
Christian




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Re: [galaxy-dev] Unable to up Planemo against latest dev

[Christian Brenninkmeijer]

I was referring to Galaxy's requirements .txt

This appears to be an issue with changes made to galaxy last weekend.

The very same Planemo work with 

commit 1aecca7889681ad9518e26e2a62b470809d2cdd1
Author: Björn Grüning <bjo...@gruenings.eu>
Date:   Sat Nov 14 23:56:19 2015 +0100

But fails at or BEFORE

commit b19e71ec465c7145840acf684f8f09eeebb99b5a
Author: Nicola Soranzo <nicola.sora...@tgac.ac.uk>
Date:   Mon Nov 16 14:57:53 2015 +

Christian

From: Peter Cock [p.j.a.c...@googlemail.com]
Sent: Friday, November 20, 2015 12:41 PM
To: Christian Brenninkmeijer
Cc: John Chilton; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Unable to up Planemo against latest dev

Which file are you looking at? There is no nose entry here:

https://github.com/galaxyproject/planemo/blob/master/requirements.txt

Perhaps a more recent version of nose is needed?

Peter

On Fri, Nov 20, 2015 at 11:51 AM, Christian Brenninkmeijer
<christian.brenninkmei...@manchester.ac.uk> wrote:
> Hi Peter/ John
> requirementx.txt already includes the latest version of nose
>
> nose==1.3.7
>
> It is nose that is complaining it does not like the sys,args passed in by 
> FunctionalTest.py
>
> Christian
>
> 
> From: Peter Cock [p.j.a.c...@googlemail.com]
> Sent: Friday, November 20, 2015 11:30 AM
> To: Christian Brenninkmeijer; John Chilton
> Cc: galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Unable to up Planemo against latest dev
>
> On Fri, Nov 20, 2015 at 9:59 AM, Christian Brenninkmeijer
> <christian.brenninkmei...@manchester.ac.uk> wrote:
>> Hi All,
>>
>> I am unable to run Planemo against the latest dev branch.
>>
>> 1. import twill error
>>
>> I was able to fix this by adding to requirements.txt
>> twill==1.8.0
>> lxml==3.5.0
>> cssselect==0.9.1
>>
>> But then I get
>>
>> functional_tests.py: error: no such option: --with-nosehtml
>> functional_tests.py ERROR 2015-11-20 09:57:23,066 Failure running tests
>> Traceback (most recent call last):
>> ...
>> SystemExit: 2
>
> That's not a very helpful error, is it? It reminds me of a missing
> dependency / installation problem I had long ago when first
> setting up TravisCI to run Galaxy tool tests:
>
> https://github.com/peterjc/pico_galaxy/commit/c8265f4a42caf62eb3bc8b36b475f16cc06f1944#diff-354f30a63fb0907d4ad57269548329e3R126
>
> @John: My guess is we need to add "nose" to planemo's requirements.txt
> to ensure this gets installed automatically?
>
> Peter
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[galaxy-dev] Unable to up Planemo against latest dev

[Christian Brenninkmeijer]

Hi All,

I am unable to run Planemo against the latest dev branch.

1. import twill error

I was able to fix this by adding to requirements.txt
twill==1.8.0
lxml==3.5.0
cssselect==0.9.1

But then I get

functional_tests.py: error: no such option: --with-nosehtml
functional_tests.py ERROR 2015-11-20 09:57:23,066 Failure running tests
Traceback (most recent call last):
  File "./scripts/functional_tests.py", line 494, in main
success = _run_functional_test( )
  File "./scripts/functional_tests.py", line 454, in _run_functional_test
test_config.configure( sys.argv )
  File 
"/home/christian/galaxy_new/.venv/local/lib/python2.7/site-packages/nose/config.py",
 line 281, in configure
options, args = self._parseArgs(argv, cfg_files)
  File 
"/home/christian/galaxy_new/.venv/local/lib/python2.7/site-packages/nose/config.py",
 line 269, in _parseArgs
return parser.parseArgsAndConfigFiles(argv[1:], cfg_files)
  File 
"/home/christian/galaxy_new/.venv/local/lib/python2.7/site-packages/nose/config.py",
 line 138, in parseArgsAndConfigFiles
return self._parser.parse_args(args, values)
  File "/usr/lib/python2.7/optparse.py", line 1402, in parse_args
self.error(str(err))
  File "/usr/lib/python2.7/optparse.py", line 1584, in error
self.exit(2, "%s: error: %s\n" % (self.get_prog_name(), msg))
  File "/usr/lib/python2.7/optparse.py", line 1574, in exit
sys.exit(status)
SystemExit: 2


Christian
University of Manchester
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Re: [galaxy-dev] Unable to up Planemo against latest dev

[Christian Brenninkmeijer]

Hi Peter/ John
requirementx.txt already includes the latest version of nose

nose==1.3.7

It is nose that is complaining it does not like the sys,args passed in by 
FunctionalTest.py

Christian
 

From: Peter Cock [p.j.a.c...@googlemail.com]
Sent: Friday, November 20, 2015 11:30 AM
To: Christian Brenninkmeijer; John Chilton
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Unable to up Planemo against latest dev

On Fri, Nov 20, 2015 at 9:59 AM, Christian Brenninkmeijer
<christian.brenninkmei...@manchester.ac.uk> wrote:
> Hi All,
>
> I am unable to run Planemo against the latest dev branch.
>
> 1. import twill error
>
> I was able to fix this by adding to requirements.txt
> twill==1.8.0
> lxml==3.5.0
> cssselect==0.9.1
>
> But then I get
>
> functional_tests.py: error: no such option: --with-nosehtml
> functional_tests.py ERROR 2015-11-20 09:57:23,066 Failure running tests
> Traceback (most recent call last):
> ...
> SystemExit: 2

That's not a very helpful error, is it? It reminds me of a missing
dependency / installation problem I had long ago when first
setting up TravisCI to run Galaxy tool tests:

https://github.com/peterjc/pico_galaxy/commit/c8265f4a42caf62eb3bc8b36b475f16cc06f1944#diff-354f30a63fb0907d4ad57269548329e3R126

@John: My guess is we need to add "nose" to planemo's requirements.txt
to ensure this gets installed automatically?

Peter
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Re: [galaxy-dev] Unable to up Planemo against latest dev

[Christian Brenninkmeijer]

Hi John,

Yes i have vitrualenv installed.

I tried planemo both using :
brew tap galaxyproject/tap
brew install planemo

And using:
virtualenv .venv; . .venv/bin/activate
pip install planemo

With the exact same results

I also have not trouble running galaxy without the extra. bit in galaxy's 
requiremets.txt

It is Planamo that fails. But only in the builds since this weekend.

Early Galaxy builds work fine.

Christian

PS.
Ubuntu and python 2.7



From: John Chilton [jmchil...@gmail.com]
Sent: Friday, November 20, 2015 2:53 PM
To: Christian Brenninkmeijer
Cc: Peter Cock; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Unable to up Planemo against latest dev

Do you have virtualenv installed and available to planemo? If not,
might be worth reviewing this thread -
http://dev.list.galaxyproject.org/Planemo-0-20-0-and-xunit-td4668334.html
and installing it.

In dev, virtualenv is a hard dependency for running Galaxy and this is
new, in the past Galaxy would run without it. We (Nate) may find a way
around this before the next release (16.01) specifically to allow
Galaxy to run in anaconda based environments.

If you have virtualenv installed, I really don't think Galaxy's
dependency list should require modification especially for Python 2.7,
is this for Linux or Mac OS X?

-John

On Fri, Nov 20, 2015 at 2:27 PM, Christian Brenninkmeijer
<christian.brenninkmei...@manchester.ac.uk> wrote:
> I have gotten past this stage and an now getting errors which may be my own.
>
> The fix was to edit
> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/dependencies/requirements.txt
> and add
> twill==1.8.0
> lxml==3.5.0
> cssselect==0.9.1
> NoseHTML==0.4.2
>
> There may well be other missing as well so that needs a look.
> For example in the old version I found an egg
> NoseTestDiff-0.1-py2.7.egg
>
> Christian
> 
> From: Peter Cock [p.j.a.c...@googlemail.com]
> Sent: Friday, November 20, 2015 12:41 PM
> To: Christian Brenninkmeijer
> Cc: John Chilton; galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Unable to up Planemo against latest dev
>
> Which file are you looking at? There is no nose entry here:
>
> https://github.com/galaxyproject/planemo/blob/master/requirements.txt
>
> Perhaps a more recent version of nose is needed?
>
> Peter
>
> On Fri, Nov 20, 2015 at 11:51 AM, Christian Brenninkmeijer
> <christian.brenninkmei...@manchester.ac.uk> wrote:
>> Hi Peter/ John
>> requirementx.txt already includes the latest version of nose
>>
>> nose==1.3.7
>>
>> It is nose that is complaining it does not like the sys,args passed in by 
>> FunctionalTest.py
>>
>> Christian
>>
>> 
>> From: Peter Cock [p.j.a.c...@googlemail.com]
>> Sent: Friday, November 20, 2015 11:30 AM
>> To: Christian Brenninkmeijer; John Chilton
>> Cc: galaxy-dev@lists.galaxyproject.org
>> Subject: Re: [galaxy-dev] Unable to up Planemo against latest dev
>>
>> On Fri, Nov 20, 2015 at 9:59 AM, Christian Brenninkmeijer
>> <christian.brenninkmei...@manchester.ac.uk> wrote:
>>> Hi All,
>>>
>>> I am unable to run Planemo against the latest dev branch.
>>>
>>> 1. import twill error
>>>
>>> I was able to fix this by adding to requirements.txt
>>> twill==1.8.0
>>> lxml==3.5.0
>>> cssselect==0.9.1
>>>
>>> But then I get
>>>
>>> functional_tests.py: error: no such option: --with-nosehtml
>>> functional_tests.py ERROR 2015-11-20 09:57:23,066 Failure running tests
>>> Traceback (most recent call last):
>>> ...
>>> SystemExit: 2
>>
>> That's not a very helpful error, is it? It reminds me of a missing
>> dependency / installation problem I had long ago when first
>> setting up TravisCI to run Galaxy tool tests:
>>
>> https://github.com/peterjc/pico_galaxy/commit/c8265f4a42caf62eb3bc8b36b475f16cc06f1944#diff-354f30a63fb0907d4ad57269548329e3R126
>>
>> @John: My guess is we need to add "nose" to planemo's requirements.txt
>> to ensure this gets installed automatically?
>>
>> Peter
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Re: [galaxy-dev] Unable to up Planemo against latest dev

[Christian Brenninkmeijer]

Confirmed with a fresh galaxy checkout
commit 05ed245353331489ee443ac483b1569dab38f500
Author: Dannon Baker <dannon.ba...@gmail.com>
Date:   Thu Nov 19 20:48:16 2015 -0500

Then ran sh.run.sh to get the updates

without the additions to requirements.txt Planemo fails.

Added the four lines.

restarted the server with sh run,sh

Noticed galaxy installing twill ect

Then Planemo test worked.

===

I don't know enough about the inner workings of Galaxy to say if the adding 
these lines to requirements.txt is the correct fix or a hack that covers a 
different bug elsewhere.

Christian

PS. I noticed that if you try to use planemo against the fresh checkout without 
starting the server with run.sh Galaxy will not fetch the required updates..
I hope that is because Planemo intentional does not check if galaxy is up to 
date to safe test time. In which case I agree!



From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
Sent: Friday, November 20, 2015 3:25 PM
To: John Chilton
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Unable to up Planemo against latest dev

Hi John,

Yes i have vitrualenv installed.

I tried planemo both using :
brew tap galaxyproject/tap
brew install planemo

And using:
virtualenv .venv; . .venv/bin/activate
pip install planemo

With the exact same results

I also have not trouble running galaxy without the extra. bit in galaxy's 
requiremets.txt

It is Planamo that fails. But only in the builds since this weekend.

Early Galaxy builds work fine.

Christian

PS.
Ubuntu and python 2.7



From: John Chilton [jmchil...@gmail.com]
Sent: Friday, November 20, 2015 2:53 PM
To: Christian Brenninkmeijer
Cc: Peter Cock; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Unable to up Planemo against latest dev

Do you have virtualenv installed and available to planemo? If not,
might be worth reviewing this thread -
http://dev.list.galaxyproject.org/Planemo-0-20-0-and-xunit-td4668334.html
and installing it.

In dev, virtualenv is a hard dependency for running Galaxy and this is
new, in the past Galaxy would run without it. We (Nate) may find a way
around this before the next release (16.01) specifically to allow
Galaxy to run in anaconda based environments.

If you have virtualenv installed, I really don't think Galaxy's
dependency list should require modification especially for Python 2.7,
is this for Linux or Mac OS X?

-John

On Fri, Nov 20, 2015 at 2:27 PM, Christian Brenninkmeijer
<christian.brenninkmei...@manchester.ac.uk> wrote:
> I have gotten past this stage and an now getting errors which may be my own.
>
> The fix was to edit
> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/dependencies/requirements.txt
> and add
> twill==1.8.0
> lxml==3.5.0
> cssselect==0.9.1
> NoseHTML==0.4.2
>
> There may well be other missing as well so that needs a look.
> For example in the old version I found an egg
> NoseTestDiff-0.1-py2.7.egg
>
> Christian
> 
> From: Peter Cock [p.j.a.c...@googlemail.com]
> Sent: Friday, November 20, 2015 12:41 PM
> To: Christian Brenninkmeijer
> Cc: John Chilton; galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Unable to up Planemo against latest dev
>
> Which file are you looking at? There is no nose entry here:
>
> https://github.com/galaxyproject/planemo/blob/master/requirements.txt
>
> Perhaps a more recent version of nose is needed?
>
> Peter
>
> On Fri, Nov 20, 2015 at 11:51 AM, Christian Brenninkmeijer
> <christian.brenninkmei...@manchester.ac.uk> wrote:
>> Hi Peter/ John
>> requirementx.txt already includes the latest version of nose
>>
>> nose==1.3.7
>>
>> It is nose that is complaining it does not like the sys,args passed in by 
>> FunctionalTest.py
>>
>> Christian
>>
>> 
>> From: Peter Cock [p.j.a.c...@googlemail.com]
>> Sent: Friday, November 20, 2015 11:30 AM
>> To: Christian Brenninkmeijer; John Chilton
>> Cc: galaxy-dev@lists.galaxyproject.org
>> Subject: Re: [galaxy-dev] Unable to up Planemo against latest dev
>>
>> On Fri, Nov 20, 2015 at 9:59 AM, Christian Brenninkmeijer
>> <christian.brenninkmei...@manchester.ac.uk> wrote:
>>> Hi All,
>>>
>>> I am unable to run Planemo against the latest dev branch.
>>>
>>> 1. import twill error
>>>
>>> I was able to fix this by adding to requirements.txt
>>> twill==1.8.0
>>> lxml==3.5.0
>>> cssselect==0.9.1
>>>
>>> But then I get
>>>
>>> functional_tests.py: err

[galaxy-dev] Bug when reading in tab seperated files

[Christian Brenninkmeijer]

Hi All,

I noticed there is a bug when you read in tab separated files and leave them as 
type auto.

These are then identified by
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/tabular.py
as "CSV" as the CSV type uses the python module "csv" which can read tab 
separated files.

Fine so far EXCEPT that CSV's set_meta method does not read columns correctly 
if tab separated.
def set_meta( self, dataset, **kwd ):
...
reader = csv.reader(csvfile)#line 920

The default delimiter for ythins csv module is comma so a tab separated file  
file will have only 1 column.

As a result especially in Planemo parameters of type type="data_column" will 
not work as the systems thinks there is only one column in the data.

==

The CSV data type needs to be fixed or to protect backward compatibility 
replaced.

There are then several options for comma separated files.

1. Use python csv's sniff method to detect the delimiter in set_meta.
This will result in a slow down and effect backward compatability.

2. Make CSV handle only comma separated files.
Improve the def sniff( self, filename ): method (line 907) to make sure it is 
comma separated.
There are various clean ways of doing this.

3. Create a new True_CSV type that sniffs only comma separated files but leave 
the old one for backward compatibility.


For tab separated files

1. Above works here too

4 Then allow the default tabular to handle tab separated files.

5. Add a new type which extends True_CSV to sniff for tab separations and 
get_meta correctly with tabs.

===
I have code that works for True_CSV and the new TSV type if that is the best 
option.

Christian
University of Manchester

3b. Add one or more new types to handle tab separated files using pythons csv 
but informing python's csv reader of the new delimiter or dialect.


regards
Christian

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Re: [galaxy-dev] recurring issues with revisions of packages from toolshed

[Christian Brenninkmeijer]

Regarding package dependency.
Assume there packages A, B and C
B depends on A and C on A and B

At the Start there is
A0, B0 and C0
B0 depends on A0 and C0 on A0 and B0

Now if A is updated there is a A1
But B0 still depends on A0 and C0 still on A0 and B0

Now if C is updated you have C1
C1 detects the latest versions of A and B so depends on A1 and B0
But B0 still depends on A0

The result is that C1 directly depends on A1 and indirectly (via B0) on A0

Could the tool shed detect this double dependency and refuse to load C1 unless 
it specifically references A0 and B0

===
Regard R 
I agree that as a wrapper it Galaxy is highly dependent on what the underlying 
tools report.

And if they change what they report that is a disaster.

What I do in my testing is after all the R is loaded try to run an R script 
which loads the packages as a test.

Something like:
library(Cairo)
args<-commandArgs(TRUE)
writeLines(capture.output(sessionInfo()), args[1])
sessionInfo()

But even then the tool goes green with an R error,

Christian


From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Thursday, October 15, 2015 10:48 AM
To: Christian Brenninkmeijer; Sarah DIEHL; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] recurring issues with revisions of packages from 
toolshed

Am 15.10.2015 um 11:43 schrieb Christian Brenninkmeijer:
> Note these are personal views of another admin not official Galaxy views.
>
> The version issues is a hard one to solve, as automatically updating upstream 
> project is also dangerous as that leaves them in a state that has not be 
> verified by the developer.
>
> Best solution could be for the toolshed to warn if a tool upload would pull 
> in multiple versions.

Can you elaborate there a little bit more?

> As for the R install issue.
> 1. I too find it extremely frustrating how often Galaxy just silently fails.

We are working on this.

https://github.com/bgruening/galaxy/pull/8

But it is really hard to convince R to provide us with a real error
code. I spend several days, but different R versions, fail differently
or not at all ..

I will keep you posted on this and hopefully the latest idea from us
works out.

Sorry for any inconvenience,
Bjoern

> 2. It could be due to a missing R package.
> The galaxy tool to determine required R packages appears to miss ones only 
> listed as linked in.
> For example I had one which depends on lme4.
> This failed to build because RcppEigen was missing
> Yet it RccpEigen is only listed as "LinkingTo:"
>
> Christian
> 
> From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
> Sarah DIEHL [sarah.di...@uni.lu]
> Sent: Wednesday, October 14, 2015 2:05 PM
> To: galaxy-dev@lists.galaxyproject.org
> Subject: [galaxy-dev] recurring issues with revisions of packages from 
> toolshed
>
> Dear all,
>
> I continuously have several issues with tool dependency packages from the 
> toolshed and their revisions. It looks like the tools I install have 
> requirements for different revisions of the same package_xy repository. What 
> I end up with quite often is having the same package installed in multiple 
> revisions (see attached "galaxytools_multiple_revisions.jpg" screenshot). 
> When I then update the older revision, it's still listet twice and 
> additionally the tool that had the older one as a dependency now says it's 
> missing a repository dependency.
>
> Although this is already quite annoying and creates a mess within the tool 
> list, I could live with it. However, sometimes it completely messes up 
> revisions. In the second attached screenshot (numpy_revision_issue.jpg) you 
> can see that this numpy repository thinks it is revision "300877695495", but 
> it's actual location has revision "8b3a5c7061d8". This causes tools that 
> depend on revision "300877695495" to think it's there, but when the 
> dependency is resolved at runtime of the tool, numpy is not found (since it's 
> location is in a different revision's folder) and the run fails. As you can 
> also see from the screenshot, resetting the metadata doesn't do anything 
> about this. Also reinstalling doesn't work, since the database keeps the 
> faulty record and uses it upon reinstallation.
>
> I think it's a problem that when I install tools that have outdated revisions 
> of a package repository as a dependency, they don't recognize that a newer 
> version is available (and already installed), but instead insist on 
> installing the older revision, too. I don't understand why they even have 
> this strict requirement on a specific version of a package repo, and not just 
> the version of the tool inside.
>
> Btw. I also noticed that the installation of R p

Re: [galaxy-dev] Galaxy Interactive Environment devs

[Christian Brenninkmeijer]

Hi,
I attended the training session and loved the tool,
Since then I was unable to get it running on my local machine.

Are the slides and files from the training day available to try it again 
properly.

Christian
Manchester

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Björn Grüning [bjo...@gruenings.eu]
Sent: Thursday, October 15, 2015 10:02 AM
To: Sebastian Schaaf; Björn Grüning; Eric Rasche; N:
Subject: Re: [galaxy-dev] Galaxy Interactive Environment devs

>>> We are not yet on IEs,
>> No, no, no. How can this happen? ;)
> I interpret ";)" as "Indeed I remember all the issues you poor guys are
> faced with" ;)
>>
>>> but we plan to upgrade our local production
>>> instance soon (a recent version is already 'waiting' to take over),
>>> apart from other goodies we intended to allow one pro user and ourselves
>>> to use iPython's power this way.
>>> So, do I read your message correctly as 'In terms of iPython it would be
>>> best for us to wait for v15.10'? Or could we just start and do an
>>> incremental upgrade as soon as v15.10 is released?
>> 15.10 is not needed for IPython. It's running since 15.05 as I remember
>> correctly. But we improved it a bit and you should take care that you
>> use the correct Docker Image for IPython. But it should work out of the
>> box. If not, let us know :)
>>
>> Cheers,
>> Bjoern
> We'll have an eye on this, thanks for the hint. And yes: We know how to
> precisely annoy you and/or Eric ;).
>
> As it somehow picks up Eric's initial question: is your impression the
> same as mine (because of no further replies to the post) that still very
> few people use in fact the great opportunities of IEs in "non-main"
> Galaxy instances?

I have no clue how often this is used. We have 598 pulls on Docker Hub
and I know a few building there own IPython Image. It's also integrated
in Cloudman as far as I know.

Would love to have some stats and impressions from users!
Ciao,
Bjoern

> Cheers,
> Sebastian
>
>>
>>> Cheers to Texas,
>>>
>>> Sebastian
>>>
>>>
>>> Eric Rasche schrieb:
 Howdy y'all,

 I'm building some changes to the IE infrastructure that will fix some
 initial hacks we did, however they will be backwards incompatible.
 Specifically these changes will fix some of the enterprise deployment
 pains (running with an external upstream proxy like apache) and allow
 for safely running IEs on a separate host.

 I'm emailing the dev list to see if anyone else has started building
 IEs, or if it just Björn and myself. Feel free to make yourselves known
 to us so we know who to contact when we're planning new features :)

 If you're just building on top of our existing containers, this
 won't be
 an issue for you, you'll just need to rebuild your containers once we
 release 15.10 versions.

 Cheers,
 Eric

>
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Re: [galaxy-dev] recurring issues with revisions of packages from toolshed

[Christian Brenninkmeijer]

Note these are personal views of another admin not official Galaxy views.

The version issues is a hard one to solve, as automatically updating upstream 
project is also dangerous as that leaves them in a state that has not be 
verified by the developer.

Best solution could be for the toolshed to warn if a tool upload would pull in 
multiple versions.

As for the R install issue.
1. I too find it extremely frustrating how often Galaxy just silently fails.

2. It could be due to a missing R package.
The galaxy tool to determine required R packages appears to miss ones only 
listed as linked in.
For example I had one which depends on lme4.
This failed to build because RcppEigen was missing
Yet it RccpEigen is only listed as "LinkingTo:"

Christian

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Sarah DIEHL [sarah.di...@uni.lu]
Sent: Wednesday, October 14, 2015 2:05 PM
To: galaxy-dev@lists.galaxyproject.org
Subject: [galaxy-dev] recurring issues with revisions of packages from toolshed

Dear all,

I continuously have several issues with tool dependency packages from the 
toolshed and their revisions. It looks like the tools I install have 
requirements for different revisions of the same package_xy repository. What I 
end up with quite often is having the same package installed in multiple 
revisions (see attached "galaxytools_multiple_revisions.jpg" screenshot). When 
I then update the older revision, it's still listet twice and additionally the 
tool that had the older one as a dependency now says it's missing a repository 
dependency.

Although this is already quite annoying and creates a mess within the tool 
list, I could live with it. However, sometimes it completely messes up 
revisions. In the second attached screenshot (numpy_revision_issue.jpg) you can 
see that this numpy repository thinks it is revision "300877695495", but it's 
actual location has revision "8b3a5c7061d8". This causes tools that depend on 
revision "300877695495" to think it's there, but when the dependency is 
resolved at runtime of the tool, numpy is not found (since it's location is in 
a different revision's folder) and the run fails. As you can also see from the 
screenshot, resetting the metadata doesn't do anything about this. Also 
reinstalling doesn't work, since the database keeps the faulty record and uses 
it upon reinstallation.

I think it's a problem that when I install tools that have outdated revisions 
of a package repository as a dependency, they don't recognize that a newer 
version is available (and already installed), but instead insist on installing 
the older revision, too. I don't understand why they even have this strict 
requirement on a specific version of a package repo, and not just the version 
of the tool inside.

Btw. I also noticed that the installation of R packages (e.g. in 
package_dexseq_1_14) silently fails. Some of the requirements and also the 
dexseq R package itself failed the installation, but Galaxy didn't recognize 
any error and it still showed up as "Installed".

Best regards,
Sarah



Sarah Diehl
HPC System Administrator

UNIVERSITÉ DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
L-4371 Belvaux
T +352 46 66 44 5360
sarah.di...@uni.lu 
http://lcsb.uni.lu
-
This message is confidential and may contain privileged information. It is 
intended for the named recipient only. If you receive it in error please notify 
me and permanently delete the original message and any copies.
-

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Re: [galaxy-dev] Installing Cairo into Gakaxy

[Christian Brenninkmeijer]

Thanks all for the help,

Using Marius's Cairo
https://testtoolshed.g2.bx.psu.edu/view/mvdbeek/package_cairo_1_14_2/83f00b68affb

And a slightly changed R
https://testtoolshed.g2.bx.psu.edu/view/brenninc/brenninc_r_sept32105/83005a26c16f
This is based on:
https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_2_1/e36e1db5e729
Except.

I removed the option to use the zip https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.1-Linux-x86_64.tar.gz
As it has hard coded environment paths in env.sh

I used Marius's Cairo, freetype and fontconfig

regards
Christian




From: Marius van den Beek [m.vandenb...@gmail.com]
Sent: Friday, October 09, 2015 1:50 PM
To: Christian Brenninkmeijer
Cc: Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hello Christian,

this is known and fixed (https://github.com/galaxyproject/tools-iuc/pull/310),
but the toolshed needs to be updated. I am thinking that this is not the only 
problem
we currently have with cairo.
I am working on the cairo issues right now and I'll give an update once the 
things work out,
plus a brand new package_r_3_2_2_cairo, that will hopefully fix your issues.

Best,
Marius

On 9 October 2015 at 14:15, Christian Brenninkmeijer 
<christian.brenninkmei...@manchester.ac.uk<mailto:christian.brenninkmei...@manchester.ac.uk>>
 wrote:
The cairo package in the testtool shed appears to have become corrupted.

If you try to download
https://testtoolshed.g2.bx.psu.edu/view/iuc/package_cairo_1_14_2/9fe5875b0ede
or any tool that depends on that.
The first page looks fine.
The second pages as an extra dependency
iuc/1.6.7

This because the encoded version return to create that second page includes 
this for some reason.
Reported to bugs as well.

Christian

From: Björn Grüning 
[bjoern.gruen...@gmail.com<mailto:bjoern.gruen...@gmail.com>]
Sent: Tuesday, October 06, 2015 3:28 PM
To: Christian Brenninkmeijer; Björn Grüning; 
galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>; 
Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi,

Am 06.10.2015 um 15:48 schrieb Christian Brenninkmeijer:
> HI Bjorn,
>
> I now see you are bringing in libmxl2 in dexseq. As this is needed by
> various R packages and already installed by fontconfig would it be
> worth making it a first class dependency of package_r_3_2_1

We could think about this, yes. Although it is not a strict dependency of R.

> I also see that in dexseg you specifically say "libxml2 needs to be
> sourced after R"
>
> Is this not because if you source it before R the current
>  name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig
>

Yes, I have fixed this here:
https://github.com/galaxyproject/tools-iuc/pull/298

Thanks,
Bjoern

>
> Christian
>
>
>  From: Björn Grüning
> [bjoern.gruen...@gmail.com<mailto:bjoern.gruen...@gmail.com>] Sent: Tuesday, 
> October 06, 2015 2:36 PM
> To: Christian Brenninkmeijer; Björn Grüning;
> galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>;
>  Dave Bouvier Subject: Re:
> [galaxy-dev] Installing Cairo into Gakaxy
>
> Hi Christian,
>
> what is needed from the TS site? Do you have any changes that are
> needed in the cairo package or R package?
>
> For me everything is now working and the only thing you need to do is
> to specify the Rcairo tarball in your tool_dependendy file. Like
> here:
>
> https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456a8a7bbd94eca94e167c5b8
>
>  Cheers, Bjoern
>
> Am 06.10.2015 um 15:21 schrieb Christian Brenninkmeijer:
>> i finally got Cairo installed into R inside galaxy.
>>
>> As well as cairo needing fontconfig to add cairo into R also
>> requires libmxl2
>>
>> I also changed the R install. 1. Never use the zip as it has hard
>> coded environment variables in it 2. The set_environment variable
>> in the R install to "prepend_to" PKG_CONFIG_DIR and
>> PKG_CONFIG_PATH
>>
>> I have some examples in the test tool shed test section but I would
>> like to clean these up first.
>>
>> Once done I will post a link in this thread.
>>
>> Christian University of Manchester
>>  From: Björn Grüning
>> [bjoern.gruen...@gmail.com<mailto:bjoern.gruen...@gmail.com>] Sent: Sunday, 
>> September 27, 2015 10:40
>> PM To: Christian Brenninkmeijer; Bjoern Gruening;
>> galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>;
>>  Dave Bouvier Subject: Re:
>> [galaxy-dev] Installing Cairo into G

Re: [galaxy-dev] Installing Cairo into Gakaxy

[Christian Brenninkmeijer]

The cairo package in the testtool shed appears to have become corrupted.

If you try to download
https://testtoolshed.g2.bx.psu.edu/view/iuc/package_cairo_1_14_2/9fe5875b0ede
or any tool that depends on that.
The first page looks fine.
The second pages as an extra dependency
iuc/1.6.7

This because the encoded version return to create that second page includes 
this for some reason.
Reported to bugs as well.

Christian

From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Tuesday, October 06, 2015 3:28 PM
To: Christian Brenninkmeijer; Björn Grüning; 
galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi,

Am 06.10.2015 um 15:48 schrieb Christian Brenninkmeijer:
> HI Bjorn,
>
> I now see you are bringing in libmxl2 in dexseq. As this is needed by
> various R packages and already installed by fontconfig would it be
> worth making it a first class dependency of package_r_3_2_1

We could think about this, yes. Although it is not a strict dependency of R.

> I also see that in dexseg you specifically say "libxml2 needs to be
> sourced after R"
>
> Is this not because if you source it before R the current
>  name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig
>

Yes, I have fixed this here:
https://github.com/galaxyproject/tools-iuc/pull/298

Thanks,
Bjoern

>
> Christian
>
>
>  From: Björn Grüning
> [bjoern.gruen...@gmail.com] Sent: Tuesday, October 06, 2015 2:36 PM
> To: Christian Brenninkmeijer; Björn Grüning;
> galaxy-dev@lists.galaxyproject.org; Dave Bouvier Subject: Re:
> [galaxy-dev] Installing Cairo into Gakaxy
>
> Hi Christian,
>
> what is needed from the TS site? Do you have any changes that are
> needed in the cairo package or R package?
>
> For me everything is now working and the only thing you need to do is
> to specify the Rcairo tarball in your tool_dependendy file. Like
> here:
>
> https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456a8a7bbd94eca94e167c5b8
>
>  Cheers, Bjoern
>
> Am 06.10.2015 um 15:21 schrieb Christian Brenninkmeijer:
>> i finally got Cairo installed into R inside galaxy.
>>
>> As well as cairo needing fontconfig to add cairo into R also
>> requires libmxl2
>>
>> I also changed the R install. 1. Never use the zip as it has hard
>> coded environment variables in it 2. The set_environment variable
>> in the R install to "prepend_to" PKG_CONFIG_DIR and
>> PKG_CONFIG_PATH
>>
>> I have some examples in the test tool shed test section but I would
>> like to clean these up first.
>>
>> Once done I will post a link in this thread.
>>
>> Christian University of Manchester
>>  From: Björn Grüning
>> [bjoern.gruen...@gmail.com] Sent: Sunday, September 27, 2015 10:40
>> PM To: Christian Brenninkmeijer; Bjoern Gruening;
>> galaxy-dev@lists.galaxyproject.org; Dave Bouvier Subject: Re:
>> [galaxy-dev] Installing Cairo into Gakaxy
>>
>> Hi Christian,
>>
>> I think I found the problem and fixed it in the Test Tool Shed. The
>> root problem was that cairo was not compiled with fontconfig and
>> therefore the freetype-cairo module was not working properly, which
>> causes R-Cairo do give us such an unusable error message.
>>
>> I tested it with our new DEXSeq wrapper, which also needs Cairo if
>> you want to create SVGs. Have a look how to define dependencies
>> here:
>>
>> https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456a8a7bbd94eca94e167c5b8
>>
>>
>>
This PR will also help you to get all needed R packages in the correct
>> order:
>>
>> https://github.com/bioarchive/aRchive_source_code/pull/20
>>
>> Keep in mind to mirror your tarballs somewhere. BioC tends to
>> remove older tarballs.
>>
>> Let me know how it goes and I will move everything over into the
>> Main Tool Shed
>>
>> Hope this fixes your issues, Bjoern
>>
>>
>>> Thanks Guys, Help greatly appreciated.
>>>
>>> I need this as my team are thinking of using SCDE see
>>> http://pklab.med.harvard.edu/scde/index.html which uses cairo.
>>>
>>> Monday in a bank holiday here so even if you guys are super fast
>>> I will not be able to test until Tuesday.
>>>
>>> Christian University of Manchester
>>> ________ From: Bjoern Gruening
>>> [bjoern.gruen...@gmail.com] Sent: Friday, August 28, 2015 3:19
>>> PM To: Christian Brenninkmeijer;

Re: [galaxy-dev] Installing Cairo into Gakaxy

[Christian Brenninkmeijer]

i finally got Cairo installed into R inside galaxy.

As well as cairo needing fontconfig to add cairo into R also requires libmxl2

I also changed the R install.
1. Never use the zip as it has hard coded environment variables in it
2. The set_environment variable in the R install to "prepend_to" PKG_CONFIG_DIR 
and PKG_CONFIG_PATH

I have some examples in the test tool shed test section but I would like to 
clean these up first.

Once done I will post a link in this thread.

Christian
University of Manchester

From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Sunday, September 27, 2015 10:40 PM
To: Christian Brenninkmeijer; Bjoern Gruening; 
galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi Christian,

I think I found the problem and fixed it in the Test Tool Shed. The root
problem was that cairo was not compiled with fontconfig and therefore
the freetype-cairo module was not working properly, which causes R-Cairo
do give us such an unusable error message.

I tested it with our new DEXSeq wrapper, which also needs Cairo if you
want to create SVGs. Have a look how to define dependencies here:

https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456a8a7bbd94eca94e167c5b8

This PR will also help you to get all needed R packages in the correct
order:

https://github.com/bioarchive/aRchive_source_code/pull/20

Keep in mind to mirror your tarballs somewhere. BioC tends to remove
older tarballs.

Let me know how it goes and I will move everything over into the Main
Tool Shed

Hope this fixes your issues,
Bjoern


> Thanks Guys,
> Help greatly appreciated.
>
> I need this as my team are thinking of using
> SCDE see http://pklab.med.harvard.edu/scde/index.html
> which uses cairo.
>
> Monday in a bank holiday here so even if you guys are super fast I will not 
> be able to test until Tuesday.
>
> Christian
> University of Manchester
> 
> From: Bjoern Gruening [bjoern.gruen...@gmail.com]
> Sent: Friday, August 28, 2015 3:19 PM
> To: Christian Brenninkmeijer; galaxy-dev@lists.galaxyproject.org; Dave Bouvier
> Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
>
> Hi,
>
> I have CCed Dave here. He took over the maintenance of R many moons ago.
> Dave can it be that we need to include some cairo headers, shared
> objects into the tarball from docker-build?
>
> Thanks,
> Bjoern
>
> On 28.08.2015 16:16, Christian Brenninkmeijer wrote:
>> Thank you Björn for the link to the new R package which appears to include 
>> cairo.
>>
>> However I am still unable to run an R script which imports cairo
>> the following line in an R Script fails
>> library(Cairo)
>>
>> When I try to do a setup_r_enviromnent I am still getting:
>> .
>> install_environment.STDOUT DEBUG 2015-08-28 14:47:00,491 checking cairo.h 
>> usability... no
>> install_environment.STDOUT DEBUG 2015-08-28 14:47:00,506 checking for 
>> cairo.h... no
>> checking cairo.h usability... no
>> checking cairo.h presence... no
>> checking for cairo.h... no
>> configure: error: Cannot find cairo.h! Please install cairo 
>> (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly.
>> ERROR: configuration failed for package ‘Cairo’
>>
>> This time tested on the testtoolshed so directly using the iuc dependencies 
>> so using his env vars
>>
>> https://testtoolshed.g2.bx.psu.edu/view/brenninc/test_r_cairo_27aug2015/77f3bd0e4153
>>
>> tool_dependency.xml attached.
>>
>> I tried it with a new git clone (Master branch)  from this morning
>> Only setting change tool_config_file, tool_dependency_dir, 
>> tools_shed_config_file and admin_users
>>
>> Installing all the required packages manually in the order that required 
>> packages installed before the using package.
>> Including Cairo before package_3_2_1
>>
>> On an Ubuntu 14.04.LTS  (updated today)
>> Memory 15.6 GiB
>> Processor Intel Xeon(R) CPU E5-1660 v3 @ 3.00Ghz x 16
>> OS type 64-bit
>>
>> I also tried it on my laptop also with Ubuntu 14.04.LTS
>>
>> Neither machine has R or Cairo installed natively.
>>
>> Any farther help or suggestions greatly appreciated.
>>
>> Christian
>> University of Manchester
>> 
>> From: Björn Grüning [bjoern.gruen...@gmail.com]
>> Sent: Wednesday, August 26, 2015 7:19 PM
>> To: Christian Brenninkmeijer; galaxy-dev@lists.galaxyproject.org
>> Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
>>
>> Hi Christian,
>>
>> looking at the R packag

Re: [galaxy-dev] Installing Cairo into Gakaxy

[Christian Brenninkmeijer]

HI Bjorn,

I now see you are bringing in libmxl2 in dexseq.
As this is needed by various R packages and already installed by fontconfig 
would it be worth making it a first class dependency of package_r_3_2_1

I also see that in dexseg you specifically say "libxml2 needs to be sourced 
after R"

Is this not because if you source it before R the current 
 $INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig
in package_r_3_2_1  overwrites anything sourced before it!

Christian



From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Tuesday, October 06, 2015 2:36 PM
To: Christian Brenninkmeijer; Björn Grüning; 
galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi Christian,

what is needed from the TS site? Do you have any changes that are needed
in the cairo package or R package?

For me everything is now working and the only thing you need to do is to
specify the Rcairo tarball in your tool_dependendy file. Like here:

https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456a8a7bbd94eca94e167c5b8

Cheers,
Bjoern

Am 06.10.2015 um 15:21 schrieb Christian Brenninkmeijer:
> i finally got Cairo installed into R inside galaxy.
>
> As well as cairo needing fontconfig to add cairo into R also requires libmxl2
>
> I also changed the R install.
> 1. Never use the zip as it has hard coded environment variables in it
> 2. The set_environment variable in the R install to "prepend_to" 
> PKG_CONFIG_DIR and PKG_CONFIG_PATH
>
> I have some examples in the test tool shed test section but I would like to 
> clean these up first.
>
> Once done I will post a link in this thread.
>
> Christian
> University of Manchester
> 
> From: Björn Grüning [bjoern.gruen...@gmail.com]
> Sent: Sunday, September 27, 2015 10:40 PM
> To: Christian Brenninkmeijer; Bjoern Gruening; 
> galaxy-dev@lists.galaxyproject.org; Dave Bouvier
> Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
>
> Hi Christian,
>
> I think I found the problem and fixed it in the Test Tool Shed. The root
> problem was that cairo was not compiled with fontconfig and therefore
> the freetype-cairo module was not working properly, which causes R-Cairo
> do give us such an unusable error message.
>
> I tested it with our new DEXSeq wrapper, which also needs Cairo if you
> want to create SVGs. Have a look how to define dependencies here:
>
> https://github.com/galaxyproject/tools-iuc/pull/281/files#diff-98f3c4d456a8a7bbd94eca94e167c5b8
>
> This PR will also help you to get all needed R packages in the correct
> order:
>
> https://github.com/bioarchive/aRchive_source_code/pull/20
>
> Keep in mind to mirror your tarballs somewhere. BioC tends to remove
> older tarballs.
>
> Let me know how it goes and I will move everything over into the Main
> Tool Shed
>
> Hope this fixes your issues,
> Bjoern
>
>
>> Thanks Guys,
>> Help greatly appreciated.
>>
>> I need this as my team are thinking of using
>> SCDE see http://pklab.med.harvard.edu/scde/index.html
>> which uses cairo.
>>
>> Monday in a bank holiday here so even if you guys are super fast I will not 
>> be able to test until Tuesday.
>>
>> Christian
>> University of Manchester
>> 
>> From: Bjoern Gruening [bjoern.gruen...@gmail.com]
>> Sent: Friday, August 28, 2015 3:19 PM
>> To: Christian Brenninkmeijer; galaxy-dev@lists.galaxyproject.org; Dave 
>> Bouvier
>> Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
>>
>> Hi,
>>
>> I have CCed Dave here. He took over the maintenance of R many moons ago.
>> Dave can it be that we need to include some cairo headers, shared
>> objects into the tarball from docker-build?
>>
>> Thanks,
>> Bjoern
>>
>> On 28.08.2015 16:16, Christian Brenninkmeijer wrote:
>>> Thank you Björn for the link to the new R package which appears to include 
>>> cairo.
>>>
>>> However I am still unable to run an R script which imports cairo
>>> the following line in an R Script fails
>>> library(Cairo)
>>>
>>> When I try to do a setup_r_enviromnent I am still getting:
>>> .
>>> install_environment.STDOUT DEBUG 2015-08-28 14:47:00,491 checking cairo.h 
>>> usability... no
>>> install_environment.STDOUT DEBUG 2015-08-28 14:47:00,506 checking for 
>>> cairo.h... no
>>> checking cairo.h usability... no
>>> checking cairo.h presence... no
>>> checking for cairo.h... no
>>> configure: error: Cannot find cairo.h! Plea

Re: [galaxy-dev] planemo and tool dependencies

[Christian Brenninkmeijer]

Hi All,

A perfect but much harder solution would be for planemo to keep its own 
dependency database.
Which when testing tools would be checked, updated if required and then used.

But that is completely beyond anything I am interested in doing.

Christian 

From: John Chilton [jmchil...@gmail.com]
Sent: Wednesday, September 09, 2015 4:56 PM
To: Christian Brenninkmeijer
Cc: Steve Cassidy; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] planemo and tool dependencies

Thanks again for implementing this Christian and for outlining how to
maybe use it for testing. I'll try to add some support and
documentation to planemo for how to use it -
https://github.com/galaxyproject/planemo/issues/290 - it is not my
favorite long term 100% solution to this problem - but it is a
fantastic 95% solution that I think people could get a lot of traction
out of if we added some support to planemo and documented how to test
using it.

-John

On Fri, Sep 4, 2015 at 12:00 PM, Christian Brenninkmeijer
<christian.brenninkmei...@manchester.ac.uk> wrote:
> I wrote the tool because when I ran planemo it found the tool_depencecy file
> but then logged that it could not find the actual tools.
>
> So
> 1. Did you install the dependecies into the galaxy you are using to run
> planemo?
> If not my tool will not work until you do.
>
> 2. When you run the test does the log show it looked for but could not find
> python_nltk_tools?
> If not then the error is outside of the scope of the tool.
>
> Christian
> 
> From: Steve Cassidy [steve.cass...@mq.edu.au]
> Sent: Friday, September 04, 2015 11:41 AM
> To: Christian Brenninkmeijer
> Cc: galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] planemo and tool dependencies
>
> Thanks Christian,
>   I'm not sure I understand how to make use of this.  My tool dependency is
> described in an XML file which is in the same source directory as the tool
> xml and python files.  The tool xml file contains:
>
>  version="1.0">python_nltk_tools
>
> and the tool_dependencies.xml file contains the definition:
>
> 
> 
> ...
>
> how do I tell planemo to tell galaxy that it should refer to this tool
> dependency file to resolve the requirement? At the moment it's loading all
> of the tools but doesn't seem to be concerned that the requirement isn't
> met.
>
> Thanks for your help.
>
> Steve
>
>
>
> On 3 September 2015 at 18:06, Christian Brenninkmeijer
> <christian.brenninkmei...@manchester.ac.uk> wrote:
>>
>> Hi,
>>
>> I wrote an extension that will help planemo pull in tool dependencies.
>>
>> See
>> https://github.com/galaxyproject/galaxy/blob/master/lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
>>
>> It is for when the dependency was installed into galaxy but where planemo
>> is not using the database to find that tool.
>>
>> It works my helping planemo guess where the tool dependency may be.
>>
>> Hope that helps.
>> Christian
>> University of Manchester
>> 
>> From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of
>> Steve Cassidy [steve.cass...@mq.edu.au]
>> Sent: Thursday, September 03, 2015 9:00 AM
>> To: galaxy-dev@lists.galaxyproject.org
>> Subject: [galaxy-dev] planemo and tool dependencies
>>
>> Hi all,
>>   I'm trying to test some tools under planemo and can't find out how to
>> have it install tool dependencies while setting up the environment.
>>
>> The dependency is on a particular python module and we have a
>> tool_dependencies.xml file to describe it. I can't see a way to tell planemo
>> serve etc to refer to that file to get the dependencies.
>>
>> Any help appreciated.
>>
>> Steve
>>
>> --
>> Department of Computing, Macquarie University
>> http://web.science.mq.edu.au/~cassidy/
>
>
>
>
> --
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy/
>
> ___
> 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/

Re: [galaxy-dev] planemo and tool dependencies

[Christian Brenninkmeijer]

I wrote the tool because when I ran planemo it found the tool_depencecy file 
but then logged that it could not find the actual tools.

So
1. Did you install the dependecies into the galaxy you are using to run planemo?
If not my tool will not work until you do.

2. When you run the test does the log show it looked for but could not find 
python_nltk_tools?
If not then the error is outside of the scope of the tool.

Christian

From: Steve Cassidy [steve.cass...@mq.edu.au]
Sent: Friday, September 04, 2015 11:41 AM
To: Christian Brenninkmeijer
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] planemo and tool dependencies

Thanks Christian,
  I'm not sure I understand how to make use of this.  My tool dependency is 
described in an XML file which is in the same source directory as the tool xml 
and python files.  The tool xml file contains:

python_nltk_tools

and the tool_dependencies.xml file contains the definition:



...

how do I tell planemo to tell galaxy that it should refer to this tool 
dependency file to resolve the requirement? At the moment it's loading all of 
the tools but doesn't seem to be concerned that the requirement isn't met.

Thanks for your help.

Steve



On 3 September 2015 at 18:06, Christian Brenninkmeijer 
<christian.brenninkmei...@manchester.ac.uk<mailto:christian.brenninkmei...@manchester.ac.uk>>
 wrote:
Hi,

I wrote an extension that will help planemo pull in tool dependencies.

See 
https://github.com/galaxyproject/galaxy/blob/master/lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py

It is for when the dependency was installed into galaxy but where planemo is 
not using the database to find that tool.

It works my helping planemo guess where the tool dependency may be.

Hope that helps.
Christian
University of Manchester

From: galaxy-dev 
[galaxy-dev-boun...@lists.galaxyproject.org<mailto:galaxy-dev-boun...@lists.galaxyproject.org>]
 on behalf of Steve Cassidy 
[steve.cass...@mq.edu.au<mailto:steve.cass...@mq.edu.au>]
Sent: Thursday, September 03, 2015 9:00 AM
To: 
galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>
Subject: [galaxy-dev] planemo and tool dependencies

Hi all,
  I'm trying to test some tools under planemo and can't find out how to have it 
install tool dependencies while setting up the environment.

The dependency is on a particular python module and we have a 
tool_dependencies.xml file to describe it. I can't see a way to tell planemo 
serve etc to refer to that file to get the dependencies.

Any help appreciated.

Steve

--
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy/



--
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy/
___
Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] Installing Cairo into Gakaxy

[Christian Brenninkmeijer]

Doing farther testing to installing Cairo into R 

I get to the point where the follow test done by the config file fails.

gcc -std=gnu99 -o conftest.output -g -O2 
-I/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/include/cairo
 
-I/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/include/freetype2
 
-I/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/include/libpng16
 
-I/home/christian/galaxy/dependency_dir/pixman/0.32.4/iuc/package_pixman_0_32_4/873f53f1abcd/include/pixman-1
 
-I/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/include/freetype2
 conftest.c 
-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
 
-L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
 
-L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
 -lfreetype -lpng16 -lz -lcairo 
-L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
 -lfreetype

Error is:
conftest.c: In function ‘main’:
conftest.c:28:4: warning: implicit declaration of function 
‘cairo_ft_font_face_create_for_pattern’ [-Wimplicit-function-declaration]
cairo_ft_font_face_create_for_pattern(0);
^
/tmp/ccbxU9HY.o: In function `main':
/home/christian/Dropbox/Manchester/galaxy_shed_tools/test/conftest.c:28: 
undefined reference to `cairo_ft_font_face_create_for_pattern'
collect2: error: ld returned 1 exit status


So it looks like cairo is not installed properly.

Christian

PS.
conftest.c is:

/* confdefs.h */
#define PACKAGE_NAME "Cairo"
#define PACKAGE_TARNAME "cairo"
#define PACKAGE_VERSION "1.3"
#define PACKAGE_STRING "Cairo 1.3"
#define PACKAGE_BUGREPORT "simon.urba...@r-project.org"
#define PACKAGE_URL ""
#define STDC_HEADERS 1
#define HAVE_SYS_WAIT_H 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define HAVE_STRING_H 1
#define HAVE_SYS_TIME_H 1
#define HAVE_UNISTD_H 1
#define HAVE_DECL_CAIRO_IMAGE_SURFACE_GET_FORMAT 0
/* end confdefs.h.  */

#include 
#include 
int main(void) {
   cairo_ft_font_face_create_for_pattern(0);
   return 0;
}



From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
Sent: Thursday, September 03, 2015 2:34 PM
To: Bjoern Gruening; galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Thanks Bjoern,

At this point I am looking to run a tiny R script which just loads Cairo and 
reports the session Info.

Full Rscript which would be run via r_wrapper.sh
===
library(Cairo)

args<-commandArgs(TRUE)
writeLines(capture.output(sessionInfo()), args[1])
sessionInfo()


Even that fails so at the moment saying Cairo library can not be found.
This is because SCDE we want to use depends on Cairo

Christian

From: Bjoern Gruening [bjoern.gruen...@gmail.com]
Sent: Thursday, September 03, 2015 2:20 PM
To: Christian Brenninkmeijer; Bjoern Gruening; 
galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi Christian,

On 03.09.2015 15:14, Christian Brenninkmeijer wrote:
> Hi,
> Have you ever actually been able to run an rscript which uses the library 
> cairo using this build outside of docker?
> Especially on a machine that does not have a /galaxy folder?

Not sure about this, I simply don't know how R plots ... but we are able
to produce a lot of different plots in a lot of different formats.



> If so did you have to install cairo into R?
> Using Rscript -e "install.packages(c('Cairo_1.5-8.tar.gz')
> Either directly or indirect vai a tool dependency with  type="setup_r_environment">
>
> If you did install cairo into R where did you get the cairo R package from?
>
> Christian
>
> ____
> From: Bjoern Gruening [bjoern.gruen...@gmail.com]
> Sent: Thursday, September 03, 2015 1:31 PM
> To: Christian Brenninkmeijer; Björn Grüning; 
> galaxy-dev@lists.galaxyproject.org; Dave Bouvier
> Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
>
> Hi Christian,
>
> thanks for debugging. For your information we use this Docker container
> to pre-build the binaries.
>
> https://github.com/galaxyproject/docker-build/tree/master/R
>
> So this is the place we need to fix the binaries.
> Hope this helps, if I find time I will also have a look,
> Bjoern
>
> On 03.0

Re: [galaxy-dev] planemo and tool dependencies

[Christian Brenninkmeijer]

Hi,

I wrote an extension that will help planemo pull in tool dependencies.

See 
https://github.com/galaxyproject/galaxy/blob/master/lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py

It is for when the dependency was installed into galaxy but where planemo is 
not using the database to find that tool.

It works my helping planemo guess where the tool dependency may be.

Hope that helps.
Christian
University of Manchester

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Steve Cassidy [steve.cass...@mq.edu.au]
Sent: Thursday, September 03, 2015 9:00 AM
To: galaxy-dev@lists.galaxyproject.org
Subject: [galaxy-dev] planemo and tool dependencies

Hi all,
  I'm trying to test some tools under planemo and can't find out how to have it 
install tool dependencies while setting up the environment.

The dependency is on a particular python module and we have a 
tool_dependencies.xml file to describe it. I can't see a way to tell planemo 
serve etc to refer to that file to get the dependencies.

Any help appreciated.

Steve

--
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy/
___
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/

Re: [galaxy-dev] Installing Cairo into Gakaxy

[Christian Brenninkmeijer]

In the continued effort to track down the issue of installing cairo into R

I found a bug in 
https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_1_2/41f43a2064ba
which installs 
https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.1.2-Linux-x84_64.tgz

This has hard code paths in it.
For example lib//pkgconfig/cairo.pc
prefix=/galaxy/builds/Linux-x86_64/install_dir

This is then picked up by cairo's configure script resulting in cairo not being 
found as it s clearly not where galaxy said it is!

Debugging continue!

Christian
University of Manchester




From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
Sent: Wednesday, September 02, 2015 11:40 AM
To: Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

I am still having issues installing Cairo into R

I have tracked part of the problem down to:
https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.1-Linux-x86_64.tgz 
does have any include files so no headers.

https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_2_1/3d28600fc82c has:
$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig
$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig

The set_to overwrites any environment_variable PKG_CONFIG values set by other 
packages

I changed the PKG_CONFIG setting to prepend to previous values and got:

checking cairo.h usability... yes
checking cairo.h presence... yes
checking for cairo.h... yes
checking for PNG support in Cairo... yes
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,315 configure: 
CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
 
-L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
 
-L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
 -lfreetype -lpng16 -lz -lcairo
checking for ATS font support in Cairo... no
configure: 
CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
 
-L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
 
-L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
 -lfreetype -lpng16 -lz -lcairo
checking for library containing deflate... none required
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,426 checking whether Cairo 
programs can be compiled... yes
checking whether Cairo programs can be compiled... yes
checking whether cairo_image_surface_get_format is declared... no
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,499 checking for FreeType 
support in cairo... yes
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,576 checking whether 
pkg-config knows about fontconfig or freetype2... yes
checking for FreeType support in cairo... yes
checking whether FreeType needs additional flags... yes
checking whether pkg-config knows about fontconfig or freetype2... yes
checking whether additional flags work... no
configure: error: Cannot use cairo-ft backend, although cairo claims it is 
working. Please check your caito installation and/or update cairo if necessary 
or set CAIRO_CFLAGS/CAIRO_LIBS accordingly.
ERROR: configuration failed for package ‘Cairo’


For the record the full cmd to setup R is:
PATH=/home/christian/galaxy/dependency_dir/pixman/0.32.4/iuc/package_pixman_0_32_4/873f53f1abcd/bin:$PATH;
 export PATH
PIXMAN_LIB_PATH=/home/christian/galaxy/dependency_dir/pixman/0.32.4/iuc/package_pixman_0_32_4/873f53f1abcd/lib;
 export PIXMAN_LIB_PATH
PKG_CONFIG_PATH=/home/christian/galaxy/dependency_dir/pixman/0.32.4/iuc/package_pixman_0_32_4/873f53f1abcd/lib/pkgconfig:$PKG_CONFIG_PATH;
 export PKG_CONFIG_PATH
PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/bin:$PATH;
 export PATH
LIBPNG_ROOT=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6;
 export LIBPNG_ROOT
LIBPNG_LIB_PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib;
 export LIBPNG_LIB_PATH
LIBPNG_INCLUDE_PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/include;
 export LIBPNG_INCLUDE_PATH
LD_LIBRARY_PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib:$LD_LIBRARY_PATH;
 export LD_LIBRARY_PATH
PKG_CONFIG_PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib/pkgconfig:$PKG_CONFIG_PATH;
 export PKG_CONFIG_PATH
FREETYPE_LIB_PATH=/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib;
 export FREETYPE_LIB_PATH
PATH=/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2

Re: [galaxy-dev] Installing Cairo into Gakaxy

[Christian Brenninkmeijer]

Hi,
Have you ever actually been able to run an rscript which uses the library cairo 
using this build outside of docker?
Especially on a machine that does not have a /galaxy folder?

If so did you have to install cairo into R?
Using Rscript -e "install.packages(c('Cairo_1.5-8.tar.gz')
Either directly or indirect vai a tool dependency with 

If you did install cairo into R where did you get the cairo R package from?

Christian


From: Bjoern Gruening [bjoern.gruen...@gmail.com]
Sent: Thursday, September 03, 2015 1:31 PM
To: Christian Brenninkmeijer; Björn Grüning; 
galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi Christian,

thanks for debugging. For your information we use this Docker container
to pre-build the binaries.

https://github.com/galaxyproject/docker-build/tree/master/R

So this is the place we need to fix the binaries.
Hope this helps, if I find time I will also have a look,
Bjoern

On 03.09.2015 12:10, Christian Brenninkmeijer wrote:
> In the continued effort to track down the issue of installing cairo into R
>
> I found a bug in 
> https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_1_2/41f43a2064ba
> which installs 
> https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.1.2-Linux-x84_64.tgz
>
> This has hard code paths in it.
> For example lib//pkgconfig/cairo.pc
> prefix=/galaxy/builds/Linux-x86_64/install_dir
>
> This is then picked up by cairo's configure script resulting in cairo not 
> being found as it s clearly not where galaxy said it is!
>
> Debugging continue!
>
> Christian
> University of Manchester
>
>
>
> 
> From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
> Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
> Sent: Wednesday, September 02, 2015 11:40 AM
> To: Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier
> Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
>
> I am still having issues installing Cairo into R
>
> I have tracked part of the problem down to:
> https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.1-Linux-x86_64.tgz
>  does have any include files so no headers.
>
> https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_2_1/3d28600fc82c has:
>   name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig
>   name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig
>
> The set_to overwrites any environment_variable PKG_CONFIG values set by other 
> packages
>
> I changed the PKG_CONFIG setting to prepend to previous values and got:
>
> checking cairo.h usability... yes
> checking cairo.h presence... yes
> checking for cairo.h... yes
> checking for PNG support in Cairo... yes
> install_environment.STDOUT DEBUG 2015-09-02 11:27:12,315 configure: 
> CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
>  
> -L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
>  
> -L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
>  -lfreetype -lpng16 -lz -lcairo
> checking for ATS font support in Cairo... no
> configure: 
> CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
>  
> -L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
>  
> -L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
>  -lfreetype -lpng16 -lz -lcairo
> checking for library containing deflate... none required
> install_environment.STDOUT DEBUG 2015-09-02 11:27:12,426 checking whether 
> Cairo programs can be compiled... yes
> checking whether Cairo programs can be compiled... yes
> checking whether cairo_image_surface_get_format is declared... no
> install_environment.STDOUT DEBUG 2015-09-02 11:27:12,499 checking for 
> FreeType support in cairo... yes
> install_environment.STDOUT DEBUG 2015-09-02 11:27:12,576 checking whether 
> pkg-config knows about fontconfig or freetype2... yes
> checking for FreeType support in cairo... yes
> checking whether FreeType needs additional flags... yes
> checking whether pkg-config knows about fontconfig or freetype2... yes
> checking whether additional flags work... no
> configure: error: Cannot use cairo-ft backend, although cairo claims it is 
> working. Please check your caito installation and/or update cairo if 
> necessary or set CAIRO_CFLAGS/CAIRO_LIBS accordingly.
> ERROR: configuration failed for package ‘Cairo’
>

Re: [galaxy-dev] Installing Cairo into Gakaxy

[Christian Brenninkmeijer]

Thanks Bjoern,

At this point I am looking to run a tiny R script which just loads Cairo and 
reports the session Info.

Full Rscript which would be run via r_wrapper.sh
===
library(Cairo)

args<-commandArgs(TRUE)
writeLines(capture.output(sessionInfo()), args[1])
sessionInfo()


Even that fails so at the moment saying Cairo library can not be found.
This is because SCDE we want to use depends on Cairo

Christian

From: Bjoern Gruening [bjoern.gruen...@gmail.com]
Sent: Thursday, September 03, 2015 2:20 PM
To: Christian Brenninkmeijer; Bjoern Gruening; 
galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi Christian,

On 03.09.2015 15:14, Christian Brenninkmeijer wrote:
> Hi,
> Have you ever actually been able to run an rscript which uses the library 
> cairo using this build outside of docker?
> Especially on a machine that does not have a /galaxy folder?

Not sure about this, I simply don't know how R plots ... but we are able
to produce a lot of different plots in a lot of different formats.



> If so did you have to install cairo into R?
> Using Rscript -e "install.packages(c('Cairo_1.5-8.tar.gz')
> Either directly or indirect vai a tool dependency with  type="setup_r_environment">
>
> If you did install cairo into R where did you get the cairo R package from?
>
> Christian
>
> 
> From: Bjoern Gruening [bjoern.gruen...@gmail.com]
> Sent: Thursday, September 03, 2015 1:31 PM
> To: Christian Brenninkmeijer; Björn Grüning; 
> galaxy-dev@lists.galaxyproject.org; Dave Bouvier
> Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
>
> Hi Christian,
>
> thanks for debugging. For your information we use this Docker container
> to pre-build the binaries.
>
> https://github.com/galaxyproject/docker-build/tree/master/R
>
> So this is the place we need to fix the binaries.
> Hope this helps, if I find time I will also have a look,
> Bjoern
>
> On 03.09.2015 12:10, Christian Brenninkmeijer wrote:
>> In the continued effort to track down the issue of installing cairo into R
>>
>> I found a bug in 
>> https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_1_2/41f43a2064ba
>> which installs 
>> https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.1.2-Linux-x84_64.tgz
>>
>> This has hard code paths in it.
>> For example lib//pkgconfig/cairo.pc
>> prefix=/galaxy/builds/Linux-x86_64/install_dir
>>
>> This is then picked up by cairo's configure script resulting in cairo not 
>> being found as it s clearly not where galaxy said it is!
>>
>> Debugging continue!
>>
>> Christian
>> University of Manchester
>>
>>
>>
>> 
>> From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
>> Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
>> Sent: Wednesday, September 02, 2015 11:40 AM
>> To: Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier
>> Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
>>
>> I am still having issues installing Cairo into R
>>
>> I have tracked part of the problem down to:
>> https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.1-Linux-x86_64.tgz
>>  does have any include files so no headers.
>>
>> https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_2_1/3d28600fc82c has:
>>   > name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig
>>   > name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig
>>
>> The set_to overwrites any environment_variable PKG_CONFIG values set by 
>> other packages
>>
>> I changed the PKG_CONFIG setting to prepend to previous values and got:
>>
>> checking cairo.h usability... yes
>> checking cairo.h presence... yes
>> checking for cairo.h... yes
>> checking for PNG support in Cairo... yes
>> install_environment.STDOUT DEBUG 2015-09-02 11:27:12,315 configure: 
>> CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
>>  
>> -L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
>>  
>> -L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
>>  -lfreetype -lpng16 -lz -lcairo
>> checking for ATS font support in Cairo... no
>> configure: 
>> CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c2

Re: [galaxy-dev] Installing Cairo into Gakaxy

[Christian Brenninkmeijer]

CAIRO_INCLUDE_PATH=/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/include:$CAIRO_INCLUDE_PATH;
 export CAIRO_INCLUDE_PATH
PKG_CONFIG_PATH=/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib/pkgconfig:$PKG_CONFIG_PATH;
 export PKG_CONFIG_PATH
TCL_LIBRARY=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/libtcl8.4.so;
 export TCL_LIBRARY
TK_LIBRARY=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/libtk8.4.so;
 export TK_LIBRARY
R_DOC_DIR=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/R/doc;
 export R_DOC_DIR
R_HOME_DIR=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/R;
 export R_HOME_DIR
R_INCLUDE_DIR=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/R/include;
 export R_INCLUDE_DIR
R_SHARE_DIR=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/R/share;
 export R_SHARE_DIR
R_ROOT_DIR=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c;
 export R_ROOT_DIR
R_HOME=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/R;
 export R_HOME
RHOME=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/R;
 export RHOME
R_LIBS=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/R/library;
 export R_LIBS
PKG_CONFIG_DIR=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/pkgconfig:/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/share/pkgconfig:$PKG_CONFIG_DIR;
 export PKG_CONFIG_DIR
PKG_CONFIG_PATH=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/lib/pkgconfig:/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/share/pkgconfig:$PKG_CONFIG_PATH;
 export PKG_CONFIG_PATH
PATH=/home/christian/galaxy/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c/bin:$PATH;
 export PATH
PATH=$PATH:$R_HOME/bin; export PATH; 
R_LIBS=/home/christian/galaxy/dependency_dir/R_cairo/0.0.2/brenninc/test_r_cairo_27aug2015/25473b0ac364;
 export R_LIBS;
Rscript -e 
"install.packages(c('Cairo_1.5-8.tar.gz'),lib='/home/christian/galaxy/dependency_dir/R_cairo/0.0.2/brenninc/test_r_cairo_27aug2015/25473b0ac364',
 repos=NULL, dependencies=FALSE)"

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
Sent: Tuesday, September 01, 2015 12:17 PM
To: Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Thanks Björn,

Add a LD_LIBRARY_PATH does not help.

Adding
CAIRO_CFLAGS=-I/home/christian/galaxy_test/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/include/cairo;
 export  CAIRO_CFLAGS

Changes the error but does not fix the problem.

I now get:
checking cairo.h usability... yes
checking cairo.h presence... yes
checking for cairo.h... yes
checking for PNG support in Cairo... yes
install_environment.STDOUT DEBUG 2015-09-01 12:01:42,121 configure: CAIRO_LIBS=
checking for ATS font support in Cairo... no
configure: CAIRO_LIBS=
checking for library containing deflate... -lz
configure: error: Cannot compile a simple Cairo program. See config.log for 
details.


A few things I did notice.

1. package_cairo_1_12_14 uses "package_pixman_0_32_4"
while package_r_3_2_1 uses package_pixman_0_32_6

2. R install in dependecy dir for 3.2.1 does not have an include directory
example:
/galaxy_test/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c
3.1.2 R did have a inlcude directory including the cairo headers.

===

Attached is the full install log.
Note the CAIRO_CFLAGS line was hard coded into recipe_manager.py for this test.

Thanks
Christian

From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Friday, August 28, 2015 6:05 PM
To: Christian Brenninkmeijer; Bjoern Gruening; 
galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi,

can you put
/home/christian/galaxy/dependency_dir/R/3.1.2/brenninc/package_r_3_1_2/655087f549e9/include/
into your LD_LIBRARY_PATH and test if this helps?

Am 28.08.2015 um 17:12 schrieb Christian Brenninkmeijer:
> I did a
> find ~ -name cairo.h
> and it looks like the header files are being made
>
> /home/christian/galaxy_test/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/include/cairo/cairo.h
> and
> /home/christian/galaxy/dependency_dir/R/3.1.2/brenninc/package_r_3_1_2/655087f549e9/include/cairo/cairo.h
>
> So it is more a question of how to get setup_r_enviromnent to find them.
>
> Christian
> __

Re: [galaxy-dev] Installing Cairo into Gakaxy

[Christian Brenninkmeijer]

Thanks Björn,

Add a LD_LIBRARY_PATH does not help.

Adding 
CAIRO_CFLAGS=-I/home/christian/galaxy_test/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/include/cairo;
 export  CAIRO_CFLAGS

Changes the error but does not fix the problem.

I now get:
checking cairo.h usability... yes
checking cairo.h presence... yes
checking for cairo.h... yes
checking for PNG support in Cairo... yes
install_environment.STDOUT DEBUG 2015-09-01 12:01:42,121 configure: CAIRO_LIBS=
checking for ATS font support in Cairo... no
configure: CAIRO_LIBS=
checking for library containing deflate... -lz
configure: error: Cannot compile a simple Cairo program. See config.log for 
details.


A few things I did notice.

1. package_cairo_1_12_14 uses "package_pixman_0_32_4"
while package_r_3_2_1 uses package_pixman_0_32_6

2. R install in dependecy dir for 3.2.1 does not have an include directory
example:
/galaxy_test/dependency_dir/R/3.2.1/iuc/package_r_3_2_1/3d28600fc82c
3.1.2 R did have a inlcude directory including the cairo headers.

===

Attached is the full install log.
Note the CAIRO_CFLAGS line was hard coded into recipe_manager.py for this test.

Thanks
Christian

From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Friday, August 28, 2015 6:05 PM
To: Christian Brenninkmeijer; Bjoern Gruening; 
galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi,

can you put
/home/christian/galaxy/dependency_dir/R/3.1.2/brenninc/package_r_3_1_2/655087f549e9/include/
into your LD_LIBRARY_PATH and test if this helps?

Am 28.08.2015 um 17:12 schrieb Christian Brenninkmeijer:
> I did a
> find ~ -name cairo.h
> and it looks like the header files are being made
>
> /home/christian/galaxy_test/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/include/cairo/cairo.h
> and
> /home/christian/galaxy/dependency_dir/R/3.1.2/brenninc/package_r_3_1_2/655087f549e9/include/cairo/cairo.h
>
> So it is more a question of how to get setup_r_enviromnent to find them.
>
> Christian
> 
> From: Bjoern Gruening [bjoern.gruen...@gmail.com]
> Sent: Friday, August 28, 2015 3:19 PM
> To: Christian Brenninkmeijer; galaxy-dev@lists.galaxyproject.org; Dave Bouvier
> Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
>
> Hi,
>
> I have CCed Dave here. He took over the maintenance of R many moons ago.
> Dave can it be that we need to include some cairo headers, shared
> objects into the tarball from docker-build?
>
> Thanks,
> Bjoern
>
> On 28.08.2015 16:16, Christian Brenninkmeijer wrote:
>> Thank you Björn for the link to the new R package which appears to include 
>> cairo.
>>
>> However I am still unable to run an R script which imports cairo
>> the following line in an R Script fails
>> library(Cairo)
>>
>> When I try to do a setup_r_enviromnent I am still getting:
>> .
>> install_environment.STDOUT DEBUG 2015-08-28 14:47:00,491 checking cairo.h 
>> usability... no
>> install_environment.STDOUT DEBUG 2015-08-28 14:47:00,506 checking for 
>> cairo.h... no
>> checking cairo.h usability... no
>> checking cairo.h presence... no
>> checking for cairo.h... no
>> configure: error: Cannot find cairo.h! Please install cairo 
>> (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly.
>> ERROR: configuration failed for package ‘Cairo’
>>
>> This time tested on the testtoolshed so directly using the iuc dependencies 
>> so using his env vars
>>
>> https://testtoolshed.g2.bx.psu.edu/view/brenninc/test_r_cairo_27aug2015/77f3bd0e4153
>>
>> tool_dependency.xml attached.
>>
>> I tried it with a new git clone (Master branch)  from this morning
>> Only setting change tool_config_file, tool_dependency_dir, 
>> tools_shed_config_file and admin_users
>>
>> Installing all the required packages manually in the order that required 
>> packages installed before the using package.
>> Including Cairo before package_3_2_1
>>
>> On an Ubuntu 14.04.LTS  (updated today)
>> Memory 15.6 GiB
>> Processor Intel Xeon(R) CPU E5-1660 v3 @ 3.00Ghz x 16
>> OS type 64-bit
>>
>> I also tried it on my laptop also with Ubuntu 14.04.LTS
>>
>> Neither machine has R or Cairo installed natively.
>>
>> Any farther help or suggestions greatly appreciated.
>>
>> Christian
>> University of Manchester
>> 
>> From: Björn Grüning [bjoern.gruen...@gmail.com]
>> Sent: Wednesday, August 26, 2015 7:19 PM
>> To: Christian Brenninkmeijer; galaxy-dev@lists.galaxyproject.org
>> Subject:

Re: [galaxy-dev] Installing Cairo into Gakaxy

[Christian Brenninkmeijer]

Thanks Guys,
Help greatly appreciated.

I need this as my team are thinking of using 
SCDE see http://pklab.med.harvard.edu/scde/index.html
which uses cairo.

Monday in a bank holiday here so even if you guys are super fast I will not be 
able to test until Tuesday.

Christian
University of Manchester

From: Bjoern Gruening [bjoern.gruen...@gmail.com]
Sent: Friday, August 28, 2015 3:19 PM
To: Christian Brenninkmeijer; galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi,

I have CCed Dave here. He took over the maintenance of R many moons ago.
Dave can it be that we need to include some cairo headers, shared
objects into the tarball from docker-build?

Thanks,
Bjoern

On 28.08.2015 16:16, Christian Brenninkmeijer wrote:
 Thank you Björn for the link to the new R package which appears to include 
 cairo.

 However I am still unable to run an R script which imports cairo
 the following line in an R Script fails
 library(Cairo)

 When I try to do a setup_r_enviromnent I am still getting:
 .
 install_environment.STDOUT DEBUG 2015-08-28 14:47:00,491 checking cairo.h 
 usability... no
 install_environment.STDOUT DEBUG 2015-08-28 14:47:00,506 checking for 
 cairo.h... no
 checking cairo.h usability... no
 checking cairo.h presence... no
 checking for cairo.h... no
 configure: error: Cannot find cairo.h! Please install cairo 
 (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly.
 ERROR: configuration failed for package ‘Cairo’

 This time tested on the testtoolshed so directly using the iuc dependencies 
 so using his env vars

 https://testtoolshed.g2.bx.psu.edu/view/brenninc/test_r_cairo_27aug2015/77f3bd0e4153

 tool_dependency.xml attached.

 I tried it with a new git clone (Master branch)  from this morning
 Only setting change tool_config_file, tool_dependency_dir, 
 tools_shed_config_file and admin_users

 Installing all the required packages manually in the order that required 
 packages installed before the using package.
 Including Cairo before package_3_2_1

 On an Ubuntu 14.04.LTS  (updated today)
 Memory 15.6 GiB
 Processor Intel Xeon(R) CPU E5-1660 v3 @ 3.00Ghz x 16
 OS type 64-bit

 I also tried it on my laptop also with Ubuntu 14.04.LTS

 Neither machine has R or Cairo installed natively.

 Any farther help or suggestions greatly appreciated.

 Christian
 University of Manchester
 
 From: Björn Grüning [bjoern.gruen...@gmail.com]
 Sent: Wednesday, August 26, 2015 7:19 PM
 To: Christian Brenninkmeijer; galaxy-dev@lists.galaxyproject.org
 Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

 Hi Christian,

 looking at the R package and on the Docker build instructions, R seems
 to be installed with cairo support:

 https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_r_3_2_1/tool_dependencies.xml
 https://github.com/natefoo/docker-build/blob/master/R/build.sh

 Are you using the latest IUC packages?
 Your script seems to be fine, I can not spot any obvious error.
 But I don't know how your dependencies are defined and which env vars
 are exported.

 Ciao,
 Bjoern

 Am 26.08.2015 um 12:18 schrieb Christian Brenninkmeijer:
 Still looking for an example tool_dependencies.xml to install R Cairo package

 Farther update.

 package_cairo_1_12_14 needs to be at the same level as package_r_3_1_2 
 inside of setup_r_environment  without the set_environment_for_install


 I am no longer getting cairo.h No but am still getting

 checking if R was compiled with the RConn patch... no
 ...
 checking for ATS font support in Cairo... no
 
 checking whether Cairo programs can be compiled...
 ERROR: configuration failed for package ‘Cairo’

 Again updated tool_dependencies.xml attached

 Thanks

 Christian
 
 From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
 Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
 Sent: Wednesday, August 26, 2015 10:18 AM
 To: galaxy-dev ‎[galaxy-dev@lists.galaxyproject.org]‎
 Subject: [galaxy-dev] Installing Cairo into Gakaxy

 Hi All,

 Has anyone got a working example tool_dependencies.xml to install the Cairo 
 package into R.
 (I actually need a package that depends on R Cairo but the current issue is 
 Cairo)

 I am having the cairo.h not found issue

 I have cloned
 https://toolshed.g2.bx.psu.edu/view/devteam/package_cairo_1_12_14/b39299b4b6e1
 (and its dependencies)

 As well as
 https://toolshed.g2.bx.psu.edu/view/iuc/package_r_3_1_2/9f2fddb9d6e2

 I am trying to use action type=setup_r_environment
 But can not get the package_cairo to be seen by the R

 I have tried  action type=set_environment_for_install both inside and 
 outside of the setup_r_environment but it does not appear to be working,

 Full attempted tool_dependencies.xml attached,

 Thanks in advance


 Christian
 University of Manchester

Re: [galaxy-dev] Installing Cairo into Gakaxy

[Christian Brenninkmeijer]

I did a 
find ~ -name cairo.h
and it looks like the header files are being made

/home/christian/galaxy_test/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/include/cairo/cairo.h
and
/home/christian/galaxy/dependency_dir/R/3.1.2/brenninc/package_r_3_1_2/655087f549e9/include/cairo/cairo.h

So it is more a question of how to get setup_r_enviromnent to find them.

Christian

From: Bjoern Gruening [bjoern.gruen...@gmail.com]
Sent: Friday, August 28, 2015 3:19 PM
To: Christian Brenninkmeijer; galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi,

I have CCed Dave here. He took over the maintenance of R many moons ago.
Dave can it be that we need to include some cairo headers, shared
objects into the tarball from docker-build?

Thanks,
Bjoern

On 28.08.2015 16:16, Christian Brenninkmeijer wrote:
 Thank you Björn for the link to the new R package which appears to include 
 cairo.

 However I am still unable to run an R script which imports cairo
 the following line in an R Script fails
 library(Cairo)

 When I try to do a setup_r_enviromnent I am still getting:
 .
 install_environment.STDOUT DEBUG 2015-08-28 14:47:00,491 checking cairo.h 
 usability... no
 install_environment.STDOUT DEBUG 2015-08-28 14:47:00,506 checking for 
 cairo.h... no
 checking cairo.h usability... no
 checking cairo.h presence... no
 checking for cairo.h... no
 configure: error: Cannot find cairo.h! Please install cairo 
 (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly.
 ERROR: configuration failed for package ‘Cairo’

 This time tested on the testtoolshed so directly using the iuc dependencies 
 so using his env vars

 https://testtoolshed.g2.bx.psu.edu/view/brenninc/test_r_cairo_27aug2015/77f3bd0e4153

 tool_dependency.xml attached.

 I tried it with a new git clone (Master branch)  from this morning
 Only setting change tool_config_file, tool_dependency_dir, 
 tools_shed_config_file and admin_users

 Installing all the required packages manually in the order that required 
 packages installed before the using package.
 Including Cairo before package_3_2_1

 On an Ubuntu 14.04.LTS  (updated today)
 Memory 15.6 GiB
 Processor Intel Xeon(R) CPU E5-1660 v3 @ 3.00Ghz x 16
 OS type 64-bit

 I also tried it on my laptop also with Ubuntu 14.04.LTS

 Neither machine has R or Cairo installed natively.

 Any farther help or suggestions greatly appreciated.

 Christian
 University of Manchester
 
 From: Björn Grüning [bjoern.gruen...@gmail.com]
 Sent: Wednesday, August 26, 2015 7:19 PM
 To: Christian Brenninkmeijer; galaxy-dev@lists.galaxyproject.org
 Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

 Hi Christian,

 looking at the R package and on the Docker build instructions, R seems
 to be installed with cairo support:

 https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_r_3_2_1/tool_dependencies.xml
 https://github.com/natefoo/docker-build/blob/master/R/build.sh

 Are you using the latest IUC packages?
 Your script seems to be fine, I can not spot any obvious error.
 But I don't know how your dependencies are defined and which env vars
 are exported.

 Ciao,
 Bjoern

 Am 26.08.2015 um 12:18 schrieb Christian Brenninkmeijer:
 Still looking for an example tool_dependencies.xml to install R Cairo package

 Farther update.

 package_cairo_1_12_14 needs to be at the same level as package_r_3_1_2 
 inside of setup_r_environment  without the set_environment_for_install


 I am no longer getting cairo.h No but am still getting

 checking if R was compiled with the RConn patch... no
 ...
 checking for ATS font support in Cairo... no
 
 checking whether Cairo programs can be compiled...
 ERROR: configuration failed for package ‘Cairo’

 Again updated tool_dependencies.xml attached

 Thanks

 Christian
 
 From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
 Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
 Sent: Wednesday, August 26, 2015 10:18 AM
 To: galaxy-dev ‎[galaxy-dev@lists.galaxyproject.org]‎
 Subject: [galaxy-dev] Installing Cairo into Gakaxy

 Hi All,

 Has anyone got a working example tool_dependencies.xml to install the Cairo 
 package into R.
 (I actually need a package that depends on R Cairo but the current issue is 
 Cairo)

 I am having the cairo.h not found issue

 I have cloned
 https://toolshed.g2.bx.psu.edu/view/devteam/package_cairo_1_12_14/b39299b4b6e1
 (and its dependencies)

 As well as
 https://toolshed.g2.bx.psu.edu/view/iuc/package_r_3_1_2/9f2fddb9d6e2

 I am trying to use action type=setup_r_environment
 But can not get the package_cairo to be seen by the R

 I have tried  action type=set_environment_for_install both inside and 
 outside of the setup_r_environment but it does not appear to be working,

 Full attempted

Re: [galaxy-dev] Installing Cairo into Gakaxy

[Christian Brenninkmeijer]

Still looking for an example tool_dependencies.xml to install R Cairo package

Farther update.

package_cairo_1_12_14 needs to be at the same level as package_r_3_1_2 inside 
of setup_r_environment  without the set_environment_for_install


I am no longer getting cairo.h No but am still getting

checking if R was compiled with the RConn patch... no
...
checking for ATS font support in Cairo... no

checking whether Cairo programs can be compiled...
ERROR: configuration failed for package ‘Cairo’

Again updated tool_dependencies.xml attached

Thanks

Christian

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
Sent: Wednesday, August 26, 2015 10:18 AM
To: galaxy-dev ‎[galaxy-dev@lists.galaxyproject.org]‎
Subject: [galaxy-dev] Installing Cairo into Gakaxy

Hi All,

Has anyone got a working example tool_dependencies.xml to install the Cairo 
package into R.
(I actually need a package that depends on R Cairo but the current issue is 
Cairo)

I am having the cairo.h not found issue

I have cloned
https://toolshed.g2.bx.psu.edu/view/devteam/package_cairo_1_12_14/b39299b4b6e1
(and its dependencies)

As well as
https://toolshed.g2.bx.psu.edu/view/iuc/package_r_3_1_2/9f2fddb9d6e2

I am trying to use action type=setup_r_environment
But can not get the package_cairo to be seen by the R

I have tried  action type=set_environment_for_install both inside and 
outside of the setup_r_environment but it does not appear to be working,

Full attempted tool_dependencies.xml attached,

Thanks in advance


Christian
University of Manchester


?xml version=1.0?
tool_dependency
package name=R version=3.1.2
repository toolshed=http://l-unxx4770.it.manchester.ac.uk:9009/; name=package_r_3_1_2 owner=brenninc 
changeset_revision=6c7b9b5dfcae prior_installation_required=True /
/package
package name=pixman version=0.32.4
  repository changeset_revision=b9960f5771e8 name=package_pixman_0_32_4 owner=brenninc prior_installation_required=True 
  toolshed=http://l-unxx4770.it.manchester.ac.uk:9009/; /
/package
package name=libpng version=1.6.7
  repository changeset_revision=a41a47c4d03b name=package_libpng_1_6_7 owner=brenninc prior_installation_required=True 
  toolshed=http://l-unxx4770.it.manchester.ac.uk:9009/; /
/package
package name=freetype version=2.5.2
  repository changeset_revision=3fdbe217abcb name=package_freetype_2_5_2 owner=brenninc prior_installation_required=True 
  toolshed=http://l-unxx4770.it.manchester.ac.uk:9009/; /
/package
package name=cairo version=1.12.14
  repository changeset_revision=5ff3cd88e260 name=package_cairo_1_12_14 owner=brenninc prior_installation_required=True 
  toolshed=http://l-unxx4770.it.manchester.ac.uk:9009/; /
/package
package name=R_cairo version=0.0.1
install version=1.0
actions
   action type=setup_r_environment
repository changeset_revision=6c7b9b5dfcae name=package_r_3_1_2 owner=brenninc toolshed=http://l-unxx4770.it.manchester.ac.uk:9009/;
package name=R version=3.1.2 /
/repository  
repository revision=5ff3cd88e260 name=package_cairo_1_12_14 owner=brenninc prior_installation_required=True 
toolshed=http://l-unxx4770.it.manchester.ac.uk:9009/;
package name=cairo version=1.12.14 /
/repository
packagehttps://cran.r-project.org/src/contrib/Cairo_1.5-8.tar.gz/package
/action
/actions
/install
/package
/tool_dependency


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[galaxy-dev] Installing Cairo into Gakaxy

[Christian Brenninkmeijer]

Hi All,

Has anyone got a working example tool_dependencies.xml to install the Cairo 
package into R.
(I actually need a package that depends on R Cairo but the current issue is 
Cairo)

I am having the cairo.h not found issue

I have cloned
https://toolshed.g2.bx.psu.edu/view/devteam/package_cairo_1_12_14/b39299b4b6e1
(and its dependencies)

As well as
https://toolshed.g2.bx.psu.edu/view/iuc/package_r_3_1_2/9f2fddb9d6e2

I am trying to use action type=setup_r_environment
But can not get the package_cairo to be seen by the R

I have tried  action type=set_environment_for_install both inside and 
outside of the setup_r_environment but it does not appear to be working,

Full attempted tool_dependencies.xml attached,

Thanks in advance


Christian
University of Manchester


?xml version=1.0?
tool_dependency
package name=R version=3.1.2
repository toolshed=http://l-unxx4770.it.manchester.ac.uk:9009/; name=package_r_3_1_2 owner=brenninc 
changeset_revision=6c7b9b5dfcae prior_installation_required=True /
/package
package name=pixman version=0.32.4
  repository changeset_revision=b9960f5771e8 name=package_pixman_0_32_4 owner=brenninc prior_installation_required=True 
  toolshed=http://l-unxx4770.it.manchester.ac.uk:9009/; /
/package
package name=libpng version=1.6.7
  repository changeset_revision=a41a47c4d03b name=package_libpng_1_6_7 owner=brenninc prior_installation_required=True 
  toolshed=http://l-unxx4770.it.manchester.ac.uk:9009/; /
/package
package name=freetype version=2.5.2
  repository changeset_revision=3fdbe217abcb name=package_freetype_2_5_2 owner=brenninc prior_installation_required=True 
  toolshed=http://l-unxx4770.it.manchester.ac.uk:9009/; /
/package
package name=cairo version=1.12.14
  repository changeset_revision=5ff3cd88e260 name=package_cairo_1_12_14 owner=brenninc prior_installation_required=True 
  toolshed=http://l-unxx4770.it.manchester.ac.uk:9009/; /
/package
package name=R_cairo version=0.0.1
install version=1.0
actions
   action type=setup_r_environment
repository changeset_revision=6c7b9b5dfcae name=package_r_3_1_2 owner=brenninc toolshed=http://l-unxx4770.it.manchester.ac.uk:9009/;
package name=R version=3.1.2 /
/repository  
action type=set_environment_for_install
 repository revision=5ff3cd88e260 name=package_cairo_1_12_14 owner=brenninc prior_installation_required=True 
 toolshed=http://l-unxx4770.it.manchester.ac.uk:9009/;
package name=cairo version=1.12.14 /
 /repository
/action
packagehttps://cran.r-project.org/src/contrib/Cairo_1.5-8.tar.gz/package
/action
/actions
/install
/package
/tool_dependency


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Re: [galaxy-dev] Slow repsonses viewing histories

[Christian Brenninkmeijer]

Hi Richard,

I am relatively new to galaxy so if you get a different response from one of 
the core team ignore this.

One thing I would check is the underlying database.
What do you have set for database_connection in your galaxy.ini file.

Especially if you are using the default sqlite this could be the issue. As that 
is store in a single file on disk.

Whichever database you have make sure it has enough resources to handle what 
will now be a large size.

Christian

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Poole, Richard [r.po...@ucl.ac.uk]
Sent: Wednesday, July 08, 2015 9:04 PM
To: galaxy-dev@lists.galaxyproject.org
Subject: [galaxy-dev] Slow repsonses viewing histories

Hi all,

I am having trouble right now with my own personal account on my production 
server. Grid refreshes are taking a huge amount of time (e.g. when viewing 
‘saved histories’ or even generating the dataset list for a single history). My 
account is very full of data (1TB), could it be this?

There are no obvious messages in the logs though so I am a bit stumped as to 
why.I do not have the same trouble when impersonating other users with fairly 
full accounts. Perhaps a database issue (I do not know how to ‘cleanup’ the 
database or indeed Galaxy user accounts). Any thoughts?

Thanks,
Richard

Richard J Poole PhD
Wellcome Trust Fellow
Department of Cell and Developmental Biology
University College London
21 University Street, London WC1E 6DE
Office (518 Rockefeller): +44 20 7679 6577 (int. 46577)
Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133)

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Re: [galaxy-dev] Problem finding depency for none toolshed tools

[Christian Brenninkmeijer]

Hi All,


I have withdrawn the pull request after useful comments from [X] Nicola Soranzo 
and John Chilton and upon finding a bug that results in a worse error in testing

I have had another go at adding this feature.
This time as a new resolver to be plugged in.

Adding at John Chilton suggestion ranking in cases where more that one possible 
revision of the same dependency can be found.

I have the code in a fork:
https://github.com/Christian-B/galaxy/blob/dev/lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py

If I want to submit a pull request is this best done against master or dev?
Also should I submit a Jira(ish) ticket for this as well? If so where?

Christian

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
Sent: Wednesday, July 01, 2015 1:17 PM
To: galaxy-dev@lists.galaxyproject.org
Subject: [galaxy-dev] Problem finding depency for none toolshed tools

Hi,
I have been testing tools not yet ready for a tool-shed but had trouble finding 
the dependencies as there was no database entries to load these.


The code in lib/galaxy/tools/deps/resolvers/galaxy_packages.py assumes that the 
env.sh or bin directory will be in dependency_dir/package/version when in fact 
it is often in dependency_dir/
package/version/owner/package_name/revision.


I have created a pull request with some code to find the dependency in the sub 
directory

https://github.com/galaxyproject/galaxy/pull/413

As I am relatively new to galaxy I have probably broken lots of 
rules/agreements on how I did the pull request. If so please let me know where 
I went wrong so I can redo it properly.

Christian

PS.
This is my proposed change to 
lib/galaxy/tools/deps/resolvers/galaxy_packages.py:
def _find_dep_versioned( self, name, version, type='package', **kwds ):
#First try the way without owner/name/revision
path = join( self.base_path, name, version )
package = self._galaxy_package_dep(path, version)
if package != INDETERMINATE_DEPENDENCY:
return package
#now try with an owner/name/revision
for owner in listdir(path):
owner_path = path + / + owner
for package_name in listdir(owner_path):
if package_name.startswith(package_+name):
package_path = owner_path + / + package_name
for revision in listdir(package_path):
revision_path = package_path + / + revision
package = self._galaxy_package_dep(revision_path, 
version)
if package != INDETERMINATE_DEPENDENCY:
return package
return INDETERMINATE_DEPENDENCY

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[galaxy-dev] Problem finding depency for none toolshed tools

[Christian Brenninkmeijer]

Hi,
I have been testing tools not yet ready for a tool-shed but had trouble finding 
the dependencies as there was no database entries to load these.


The code in lib/galaxy/tools/deps/resolvers/galaxy_packages.py assumes that the 
env.sh or bin directory will be in dependency_dir/package/version when in fact 
it is often in dependency_dir/
package/version/owner/package_name/revision.


I have created a pull request with some code to find the dependency in the sub 
directory

https://github.com/galaxyproject/galaxy/pull/413

As I am relatively new to galaxy I have probably broken lots of 
rules/agreements on how I did the pull request. If so please let me know where 
I went wrong so I can redo it properly.

Christian

PS.
This is my proposed change to 
lib/galaxy/tools/deps/resolvers/galaxy_packages.py:
def _find_dep_versioned( self, name, version, type='package', **kwds ):
#First try the way without owner/name/revision
path = join( self.base_path, name, version )
package = self._galaxy_package_dep(path, version)
if package != INDETERMINATE_DEPENDENCY:
return package
#now try with an owner/name/revision
for owner in listdir(path):
owner_path = path + / + owner
for package_name in listdir(owner_path):
if package_name.startswith(package_+name):
package_path = owner_path + / + package_name
for revision in listdir(package_path):
revision_path = package_path + / + revision
package = self._galaxy_package_dep(revision_path, 
version)
if package != INDETERMINATE_DEPENDENCY:
return package
return INDETERMINATE_DEPENDENCY

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Re: [galaxy-dev] errors and questions with run_tests.sh and install_and_test_tool_shed_repositories.sh

[Christian Brenninkmeijer]

Hi,
I am relatively new to Galaxy so if you get a difference answer from a core 
developer consider that one.

Personally I never got the  run_test.sh -id ...) to run  but I did use

planemo

http://planemo.readthedocs.org/en/latest/readme.html

With success.  It is much easier, does not need the tool to be installed in a 
local galaxy to test.

It does require the tool xml config file
See: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

And depends on their being a tests section.

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

Christian
University of Manchester

PS. I am not a developer of Planemo just a user so please keep all question on 
this mailing list

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Loraine Guéguen [loraine.gueg...@sb-roscoff.fr]
Sent: Tuesday, June 02, 2015 9:14 AM
To: Galaxy Dev List
Subject: [galaxy-dev] errors and questions with run_tests.sh and 
install_and_test_tool_shed_repositories.sh

Hi,

I have investigated the testing possibilities within a Galaxy local instance 
and within a toolshed. I met some difficulties and I have 4 questions listed 
below.


1- Tests on tools installed in a local Galaxy instance (with run_tests.sh) : It 
seems that it is only possible to test the tools that have been manually 
installed (run_test.sh -id ...), not the tools that have been installed through 
a toolshed. Is that true ? When I try to launch the tests of a toolshed 
installed tool, I have the following error message :

#

Failure: ValueError (No such test TestForTool_sartools_edger) ... ERROR
==
ERROR: Failure: ValueError (No such test TestForTool_sartools_edger)
--
Traceback (most recent call last):
  File 
/projet/htdocs/galaxy-dev/galaxy-dist/eggs/nose-0.11.1-py2.7.egg/nose/failure.py,
 line 39, in runTest
raise self.exc_class(self.exc_val)
ValueError: No such test TestForTool_sartools_edger

--
Ran 1 test in 0.002s
FAILED (errors=1)

#


2- Tests on tools installed in a local Galaxy instance (with run_tests.sh) : Is 
it possible to test tools which have repository or tool dependencies ? I have a 
tool (manually installed in galaxy-dist/tools/) with a dependence to a datatype 
installed from a toolshed. The datatype (no_unzip.zip) is defined in the 
param input tag (in test) with attribute ftype. When running 
run_tests.sh, it seems that the dataype is not known :

#

==
ERROR: test_tool_01 (functional.test_toolbox.TestForTool_sartools_edger)
SARTools edgeR ( sartools_edger )  Test-2
--
Traceback (most recent call last):
  File /w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py, 
line 268, in test_tool
self.do_it( td )
  File /w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py, 
line 37, in do_it
stage_data_in_history( galaxy_interactor, testdef.test_data(), 
test_history, shed_tool_id )
  File /w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py, line 36, 
in stage_data_in_history
upload_waits.append( galaxy_interactor.stage_data_async( test_data, 
history, shed_tool_id ) )
  File /w/galaxy/galaxy4loraine/galaxy-dist/test/base/interactor.py, line 
182, in stage_data_async
raise Exception(submit_response)
Exception: {u'message': {u'type': u'error', u'data': {u'file_type': uAn 
invalid option was selected for file_type, u'no_unzip.zip', please verify., 
u'files_metadata': [uAn invalid option was selected for file_type, 
u'no_unzip.zip', please verify.]}}}

#


3- Toolshed Install and Test framework ( 
install_and_test_tool_shed_repositories.sh) : For my tool, the test fails if I 
don't explicitely defined the dbkey attribute to unknown (dbkey=?) in the 
param input tag (in test). The default dbkey value seems to be hg17 
(whereas hg17 is not defined on the server running my toolshed). So I have the 
following error message if I don't add dbkey=? in test :

#

==
ERROR: test_tool_01 
(functional.test_toolbox.TestForTool_galaxy4loraine:9009/repos/lgueguen/sartools_1_0_2/sartools_edger/20150209)
SARTools edgeR ( 
galaxy4loraine:9009/repos/lgueguen/sartools_1_0_2/sartools_edger/20150209 )  
Test-2
--
Traceback (most recent call last):
  File /w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py, 
line 268, in test_tool
self.do_it( td )
  File /w/galaxy/galaxy4loraine/galaxy-dist/test/functional/test_toolbox.py, 
line 37, in do_it
stage_data_in_history( galaxy_interactor, testdef.test_data(), 

Re: [galaxy-dev] Can't set value of conditional boolean parameter in tool tests

[Christian Brenninkmeijer]

Hi Peter,

1. I would not recommend using truevalue= in boolean parm values inside of 
conditionals are the behaviour is buggy! (I will post a test example in another 
post)

2, In the when statement the boolean values must be LOWER case as in
when value=true

3. In the command the Boolean values are CAPITALIZED as in 
#if str($bdg_options.bdg2) == 'True'

3a. or better yet  do not cast to string but just do
#if $bdg_options.bdg2

Christian
University of Manchester


From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Peter Briggs [peter.bri...@manchester.ac.uk]
Sent: Tuesday, May 19, 2015 3:01 PM
To: galaxy-dev@lists.galaxyproject.org
Subject: [galaxy-dev] Can't set value of conditional boolean parameter in   
tool tests

Hello

I've encountered a problem with my tool tests when using a boolean as
the control parameter within a conditional: it doesn't appear to be
possible to change the value from the default true or false values
within the tests.

For example if I have a boolean 'bdg2' which controls a conditional
block and which defaults to its falsevalue:

   ...
   conditional name=bdg_options
 param name=bdg2 type=boolean checked=False
   truevalue=-B2 falsevalue= label=Save pileups in bedGraph? /
 when value=-B2
   ...

and then try to set the value within a test using:

 param name=bdg_options|bdg2 value=true /

then the value remains unchanged from the default when the tests are
run. (Similarly if I set checked=True then the value in the tests is
always True regardless of the value I try to set.)

I've tried various ways of referencing the parameter (e.g.
'bdg_options|bdg2', 'bdg2' and 'bdg_options') but none of these work for me.

Am I doing something obviously wrong? (nb this is a different problem
from my previous post about setting boolean values in tests - that works
fine for booleans which are not conditional control parameters).

I've made a small example tool to investigate the issue, the files are here:

https://gist.github.com/pjbriggs/c27e4366dfcdd6d96cb2

and using planemo 0.11.1 to run the tests.

(On a side note, it also seems that within the command section, the
values returned for this type of boolean only ever appear to be 'True'
or 'False' - but it seems okay to match against the truevalue and
falsevalues in the when tag.)

Thanks for any help,

Best wishes

Peter

--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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[galaxy-dev] Geting integer value from InputValueWrapper in plugin xml file

[Christian Brenninkmeijer]

Hi,
I am a new galaxy developer playing with writing my first plugins

In my plugin xml configaration file:
I want to be able to increase the value of one parameter based on another using

  command interpreter=python
#if $rows.option ==header_ignore
#set $data_start = $rows.ignore + 1

but I get:
unsupported operand type(s) for +: 'InputValueWrapper' and 'int'

A hack workaround I found was:
#set $data_start = int(str($rows.ignore)) + 1

I just wondered if there was a cleaner way to get the integer value from a 
InputValueWrapper object.

Which is set to integer by:
param name=ignore size=4 type=integer value=1 

If documentation exist somwere please send me an RTFM link.
(I didn't find it in 
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax)

Thanks in advance
Christian Brenninkmeijer
University of Manchester

Ps. If you want to see exactly what I am playing with see
https://github.com/Christian-B/galaxy_tools/tree/master/summary
(Note that is subject to change as I learn)



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