Installing Cairo into Gakaxy - galaxy-dev

26 Aug 2015

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.gruening@gmail.com
<mailto:bjoern.gruening@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
> <environment_variable action="set_to"
>
name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
>

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

Thanks,
Bjoern

>
> Christian
>
>
> ________________________________________ From: Björn Grüning
> [bjoern.gruening@gmail.com <mailto:bjoern.gruening@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.gruening@gmail.com <mailto:bjoern.gruening@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 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.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>]
Sent: Friday, August 28, 2015 3:19
>>> PM To: Christian Brenninkmeijer;
>>> galaxy-dev@lists.galaxyproject.org
<mailto: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.gruening@gmail.com
<mailto:bjoern.gruening@gmail.com>] Sent: Wednesday, August 26, 2015
>>>> 7:19 PM To: Christian Brenninkmeijer;
>>>> galaxy-dev@lists.galaxyproject.org
<mailto: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-bounces@lists.galaxyproject.org
<mailto:galaxy-dev-bounces@lists.galaxyproject.org>] on behalf of
>>>>> Christian Brenninkmeijer
>>>>> [christian.brenninkmeijer@manchester.ac.uk
<mailto:christian.brenninkmeijer@manchester.ac.uk>] Sent: Wednesday,
>>>>> August 26, 2015 10:18 AM To: galaxy-dev
>>>>> ‎[galaxy-dev@lists.galaxyproject.org
<mailto: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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ___________________________________________________________
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