Looks like you're missing cmake, a dependency for building FreeBayes.  If
you're able to install that for your system (available in most package
managers) you should be good to go.

-Dannon


On Tue, Apr 30, 2013 at 1:03 PM, Iry Witham <iry.wit...@jax.org> wrote:

>  Hi All,
>
>  I am trying to get Freebayes installed on a cloud man instance from the
> galaxy toolshed.  I have successfully installed the Samtools 0.1.18
> package, but the freebayes package errors.
>
>  The Error is:
>
>  Tool shed repository: freebayes
> Tool shed repository changeset revision: 28e422c589ac
> Tool dependency status: Error
> Tool dependency installation error: /bin/sh: cmake: not found
> make[1]: *** [../bamtools/lib/libbamtools.a] Error 127
> make: *** [all] Error 2
> Tool dependency installation directory:
> /mnt/galaxyTools/tools/freebayes/0.9.6_9608597d12e127c847ae03aa03440ab63992fedf/devteam/freebayes/28e422c589ac
>
>  I get the following message after the error occurs:
>
>  This tool dependency is not installed correctly (see the *Tool
> dependency installation error* below). Choose *Uninstall this tool
> dependency* from the *Repository Actions* menu, correct problems if
> necessary, and try installing the dependency again.
>
>  I have followed this procedure and still have the same error.  I have
> looked at the Installation.log file and this is what I found:
>
>  #############################################
> git clone --recursive git://github.com/ekg/freebayes.git
> STDOUT
> Initialized empty Git repository in
> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/.git/
> Submodule 'bamtools' (git://github.com/pezmaster31/bamtools.git)
> registered for path 'bamtools'
> Submodule 'intervaltree' (git://github.com/ekg/intervaltree.git)
> registered for path 'intervaltree'
> Submodule 'vcflib' (git://github.com/ekg/vcflib.git) registered for path
> 'vcflib'
> Initialized empty Git repository in
> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/bamtools/.git/
> Submodule path 'bamtools': checked out
> '3fe66b92028b60629826d827ee9058405fa7e4be'
> Initialized empty Git repository in
> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/intervaltree/.git/
> Submodule path 'intervaltree': checked out
> 'd151b487804861dc9f932e9f1fe4f8c499673cec'
> Initialized empty Git repository in
> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/.git/
> Submodule path 'vcflib': checked out
> '480d96e16a552d36369dc9cb2b39ceedb260944a'
> Submodule 'fastahack' (git://github.com/ekg/fastahack.git) registered for
> path 'fastahack'
> Submodule 'fsom' (git://github.com/ekg/fsom.git) registered for path
> 'fsom'
> Submodule 'intervaltree' (git://github.com/ekg/intervaltree.git)
> registered for path 'intervaltree'
> Submodule 'multichoose' (git://github.com/ekg/multichoose.git) registered
> for path 'multichoose'
> Submodule 'smithwaterman' (git://github.com/ekg/smithwaterman.git)
> registered for path 'smithwaterman'
> Submodule 'tabixpp' (git://github.com/ekg/tabixpp.git) registered for
> path 'tabixpp'
> Initialized empty Git repository in
> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/fastahack/.git/
> Submodule path 'fastahack': checked out
> '6acaf9875f2dbcdf86c9c690a8d188000e90d388'
> Initialized empty Git repository in
> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/fsom/.git/
> Submodule path 'fsom': checked out
> '1b888f32c4bd571d1a0bea88d39cd7d7f23ea4b8'
> Initialized empty Git repository in
> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/intervaltree/.git/
> Submodule path 'intervaltree': checked out
> '1290744283cef8076bb8a2968d4899b7228435f4'
> Initialized empty Git repository in
> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/multichoose/.git/
> Submodule path 'multichoose': checked out
> '73d35daa18bf35729b9ba758041a9247a72484a5'
> Initialized empty Git repository in
> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/smithwaterman/.git/
> Submodule path 'smithwaterman': checked out
> 'd9724f156c07cf16d00d251bebc20c6383eb6bde'
> Initialized empty Git repository in
> /mnt/galaxyData/tmp/tmpCUrxI7/freebayes/vcflib/tabixpp/.git/
> Submodule path 'tabixpp': checked out
> 'fbdde774adfc79ca75a65b4321b89b67cd81b921'
> #############################################
>
>  #############################################
> git clone --recursive git://github.com/ekg/freebayes.git
> STDERR
>
>  #############################################
>
>  #############################################
> git checkout 9608597d12e127c847ae03aa03440ab63992fedf
> STDOUT
> M bamtools
> M vcflib
> #############################################
>
>  #############################################
> git checkout 9608597d12e127c847ae03aa03440ab63992fedf
> STDERR
> Note: checking out '9608597d12e127c847ae03aa03440ab63992fedf'.
>
>  You are in 'detached HEAD' state. You can look around, make experimental
> changes and commit them, and you can discard any commits you make in this
> state without impacting any branches by performing another checkout.
>
>  If you want to create a new branch to retain commits you create, you may
> do so (now or later) by using -b with the checkout command again. Example:
>
>    git checkout -b new_branch_name
>
>  HEAD is now at 9608597... example pipeline script
> #############################################
>
>  #############################################
> git submodule update --recursive
> STDOUT
> Submodule path 'bamtools': checked out
> '8a5d6508d8fc52b25c9129037e44cc448bafebc7'
> Submodule path 'vcflib': checked out
> '3f0d5e19596252b858a7f6eff1578e4295f549c8'
> Submodule path 'fastahack': checked out
> 'd1bcd7a2d52ee0e2823884c8ede22ce228d3c060'
> Submodule path 'smithwaterman': checked out
> '2882633a3b89f820d692a9b3316f4891dc3a1ff8'
> #############################################
>
>  #############################################
> git submodule update --recursive
> STDERR
> warning: unable to rmdir fsom: Directory not empty
> #############################################
>
>  #############################################
> make
> STDOUT
> cd src && make
> make[1]: Entering directory `/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/src'
> cd ../bamtools && mkdir -p build && cd build && cmake .. && make
> make[1]: Leaving directory `/mnt/galaxyData/tmp/tmpCUrxI7/freebayes/src'
> #############################################
>
>  #############################################
> make
> STDERR
> /bin/sh: cmake: not found
> make[1]: *** [../bamtools/lib/libbamtools.a] Error 127
> make: *** [all] Error 2
> #############################################
>
>  Any ideas on how to resolve this?
>
>  Thanks,
>
>  Iry Witham
>
>  The information in this email, including attachments, may be
> confidential and is intended solely for the addressee(s). If you believe
> you received this email by mistake, please notify the sender by return
> email as soon as possible.
>
> ___________________________________________________________
> 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:
>   http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to