Re: [galaxy-dev] Installing Cairo into Gakaxy

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 <environment_variable action="set_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>

Christian ________________________________________ From: Björn Grüning [bjoern.gruening(a)gmail.com] Sent: Tuesday, October 06, 2015 2:36 PM To: Christian Brenninkmeijer; Björn Grüning; galaxy-dev(a)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-98f3c4d456... 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(a)gmail.com] Sent: Sunday, September 27, 2015 10:40 > PM To: Christian Brenninkmeijer; Bjoern Gruening; > galaxy-dev(a)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-98f3c4d456... > > >

> 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(a)gmail.com] Sent: Friday, August 28, 2015 3:19 >> PM To: Christian Brenninkmeijer; >> galaxy-dev(a)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_27aug2015/7... >>> >>> >>>

>>> >>> 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(a)gmail.com] Sent: Wednesday, August 26, 2015 >>> 7:19 PM To: Christian Brenninkmeijer; >>> galaxy-dev(a)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... >>> >>>

>>> >>> 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(a)lists.galaxyproject.org] on behalf of >>>> Christian Brenninkmeijer >>>> [christian.brenninkmeijer(a)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/b39299b... >>>> >>>>

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

>>>> 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 >>>> >>>> >>>> >>>> >>>> >>>> ___________________________________________________________ >>>> 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/ >>>> >>