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-packages

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
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