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

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