Peter, The problem with testing the installation of package tool dependencies, especially but not limited to BLAST+, is that the time it takes to compile them exceeds the timeout for the automated testing framework, and so it terminates that build step. I am currently working on enhancing the actions tag to support a different install process depending on the target architecture, and hope to have that ready early next week. --Dave B. On 8/14/13 06:56:35.000, Peter Cock wrote:
Hi Greg,
I'm hoping you (or Dave) can throw a little light on why the NCBI BLAST+ nightly tests are not working again yet:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/949fa0294c0d
e.g. Fatal error: Exit code 127 () /bin/sh: 1: blastn: not found /bin/sh: 1: blastn: not found
As of that commit, the ncbi_blast_plus repository depends on the new IUC repository package_blast_plus_2_2_26 which now depends on the IUC repository package_boost_1_53, which depends on Bjoern's package_bzlib_1_0, i.e. this chain:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus -> http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26 -> http://testtoolshed.g2.bx.psu.edu/view/iuc/package_boost_1_53 -> http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_bzlib_1_0
Sadly the (Test) Tool Shed isn't showing me any install logs, so I am hoping *you* have access to them.
I've also requested individual package repositories (i.e. type "Tool dependency definition") be tested nightly for installation problems: https://trello.com/c/HVGrShnC/1042-tool-shed-should-test-installation-of-pac...
Meanwhile, I have tried this locally - the dependencies seem to install, but the BLAST+ package says "Installed, missing tool dependencies". It looks like the BLAST+ make fails, but I don't know how/if I can see this from the Galaxy Admin web-interface.
I can see the logs at the command line,
$ tail -n 30 blast+/2.2.26+/iuc/package_blast_plus_2_2_26/9ff9bfdcd04f/INSTALLATION.log make[1]: Leaving directory `/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/GCC412-Debug64/build' #############################################
############################################# cd c++ && ./configure --with-boost=$BOOST_ROOT_DIR --prefix=/opt/galaxy-dist-shed-tools/blast+/2.2.26+/iuc/package_blast_plus_2_2_26/9ff9bfdcd04f && make && make install STDERR basename: missing operand Try `basename --help' for more information. configure: WARNING: Untested Boost version; may prove incompatible. configure: WARNING: If so, please re-run this script with the flag --without-boost. make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/db/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/db/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/ctools/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/ctools/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/misc/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/misc/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/gui/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/gui/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/sample/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/sample/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/internal/Makefile.in] Error 1 (ignored) make[1]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/internal/Makefile.in] Error 1 (ignored) make[2]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/corelib/test/Makefile.in] Error 1 (ignored) make[2]: [/opt/galaxy-dist/database/tmp/tmp-toolshed-mtdutx4hN/ncbi-blast-2.2.26+-src/c++/src/corelib/test/Makefile.in] Error 1 (ignored) /bin/sh: /usr/bin/touch: No such file or directory make[3]: *** [sources.usr] Error 127 make[2]: *** [sources.usr.locked] Error 2 make[1]: *** [all_r.real] Error 5 make: *** [all] Error 2 #############################################
I just checked the BOOST bit worked by manually compiling BLAST+,
$ echo 'BOOST_ROOT_DIR=/opt/galaxy-dist-shed-tools/boost/1.53.0/iuc/package_boost_1_53/a72f8efe9201/boost; export BOOST_ROOT_DIR' $ ./configure --with-boost=$BOOST_ROOT_DIR --prefix=/opt/galaxy-dist-shed-tools/blast+/2.2.26+/iuc/package_blast_plus_2_2_26/9ff9bfdcd04f ... ******* CONFIGURATION SUCCESSFUL ******* $ make ... /bin/sh: /usr/bin/touch: No such file or directory ... make: *** [all] Error 2
So sign of the basename error, but the touch problem persists. Fixed with:
$ sudo ln -s /bin/touch /usr/bin/touch
Having created the touch alias, manual compilation appears to be working (it just takes a long long time). I intend to repeat this via the Galaxy Admin page ...
However, this doesn't help with knowing what might be going wrong during the (Test) Tool Shed nightly tests.
Peter _______________________________________________ galaxy-iuc mailing list galaxy-iuc@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-iuc