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.
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