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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