I've emailed the rest of the IUC for their input - adding the old versions
in bioconda should work, or adding the recent Biopython releases as
packages on the Tool Shed.

For blast_rbh just need a semi-recent Biopython available in both systems
(until everyone moves over to bioconda - we've not yet done this on our
local Galaxy for example).

Peter

Peter

On Wed, 19 Apr 2017 at 13:04, Matthias Bernt <m.be...@ufz.de> wrote:

> Dear Peter,
>
> thanks. Just for understanding: Why not just change the biopython
> dependency from 1.67 to 1.69, if this is the one available in bioconda.
> blast_rbh seems to use only the SeqIO fasta parser and writer. This
> should be no problem.
>
> But I guess that for older versions of blast_rbh one might still need
> legacy packages of biopython. Or could one change the dependencies in
> older versions? Or would this be no good idea because of backward
> compatibility?
>
> Cheers,
> Matthias
>
>
>
>
>
> On 19.04.2017 13:50, Peter Cock wrote:
> > Just lucky timing, could you try blast_rbh v0.1.11,
> >
> > https://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh/d8d9a9069586
> >
> > For BLAST+ this ought to work with either bioconda, or the legacy XML
> > based packages, as both have BLAST+ 2.5.0.
> >
> > However, it looks like bioconda only has Biopython 1.68 and 1.69, while
> > the legacy XML based packages only go up to Biopython 1.67 at the time
> > of writing... it looks like we'll need to add a couple more legacy
> packages.
> >
> > Peter
> >
> > On Wed, Apr 19, 2017 at 12:01 PM, Matthias Bernt <m.be...@ufz.de> wrote:
> >> Dear Peter,
> >>
> >> thanks for the info. Would be great to get the update, but since I have
> a
> >> method that is working for the moment there is no need to hurry.
> >>
> >> Best,
> >> Matthias
> >>
> >>
> >>
> >> On 19.04.2017 12:57, Peter Cock wrote:
> >>>
> >>> Oh right - I've just been updating ncbi_blast_plus this morning
> >>> to transition to BLAST+ 2.5.0 via either bioconda or the older
> >>> legacy Tool Shed.
> >>>
> >>> I can try to update blast_rbh next, which may solve this by
> >>> letting you use bioconda.
> >>>
> >>> Peter
> >>>
> >>> On Wed, Apr 19, 2017 at 11:52 AM, Matthias Bernt <m.be...@ufz.de>
> wrote:
> >>>>
> >>>> Dear Marius,
> >>>>
> >>>> thanks again for the help. I'm trying to install blast_rbh (owner is
> >>>> peterjc). The dependencies look as follows:
> >>>>
> >>>> blast_rbh
> >>>> - biopython
> >>>>   - package_biopython_1_64
> >>>>     - package_numpy_1_8
> >>>>       - package_atlas_3_10
> >>>> - blast
> >>>>     - package_blast_plus_2_2_31
> >>>>       - blast+
> >>>>
> >>>> With unchecked "When available, install Tool Shed managed tool
> >>>> dependencies?" I get all as "Installed, missing tool dependencies".
> >>>> Blast_rbh is not working since blast+ is not installed. Even if I
> install
> >>>> blast+ manually (in galaxy) its not working (makeblastdb is missing).
> >>>>
> >>>> When I leave "When available, install Tool Shed managed tool
> >>>> dependencies?"
> >>>> I see blast_rbh, package_blast_plus package_biopython as installed and
> >>>> the
> >>>> others as Installed, missing tool dependencies.
> >>>> Here blast_rbh is working.
> >>>>
> >>>> What would be your suggestion? Live with the latter and file an issue
> at
> >>>> the
> >>>> tools repository (difficult to say which causes the problem(s))?
> >>>>
> >>>> I get similar behavior if I try to install from the test toolshed.
> >>>> (Only a different error from atlas: /bin/sh: line 3:
> >>>> /host/static_full_blas_lapack.diff: No such file or directory).
> >>>>
> >>>> But, actually I'm trying to automatize tool installation using the
> >>>> ansible
> >>>> role ansible-galaxy-tools
> >>>> (https://github.com/galaxyproject/ansible-galaxy-tools). With this
> method
> >>>> I
> >>>> get the latter behavior. The role uses uses ephemeris==0.4.0 to
> install
> >>>> tools. There I have seen three global variables that (I guess) control
> >>>> the
> >>>> installation of dependencies.
> >>>>
> >>>> INSTALL_TOOL_DEPENDENCIES = False
> >>>> INSTALL_REPOSITORY_DEPENDENCIES = True
> >>>> INSTALL_RESOLVER_DEPENDENCIES = True
> >>>>
> >>>> I guess I could control the behavior with the latter two variables.
> >>>>
> >>>> Best,
> >>>> Matthias
> >>>>
> >>>>
> >>>>
> >>>> On 18.04.2017 19:24, Marius van den Beek wrote:
> >>>>>
> >>>>>
> >>>>> Hi Matthias,
> >>>>>
> >>>>> it's me again!
> >>>>> What tool are you trying to install?
> >>>>>
> >>>>> My -perhaps- unhelpful suggestion is to not install anything that
> starts
> >>>>> with
> >>>>> package_* (also called tool shed packages), those should be
> exclusively
> >>>>> installed when you absolutely need
> >>>>> to install an old tool that can only function with packages.
> >>>>> We've switched to conda nowadays, which is much easier to install
> and to
> >>>>> maintain.
> >>>>> In fact the IUC has ported all their latest tools to conda, and
> >>>>> similarly most devteam
> >>>>> tools that are still in active use have also been ported to use Conda
> >>>>> dependencies.
> >>>>>
> >>>>> If you look at this
> >>>>> document
> >>>>>
> https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/,
> >>>>> there is a part where you confirm dependencies. If you click on show
> >>>>> detail, and you unselect
> >>>>> When available, install Tool Shed managed tool dependencies?
> >>>>> Galaxy will not try to install these old packages. There are some
> tools
> >>>>> which come both with
> >>>>> old toolshed dependencies and that have Conda available. You may be
> >>>>> lucky and find that
> >>>>> the tool you are trying to install has Conda dependencies available.
> >>>>> There is a lot more background on the Toolshed and Conda in this
> >>>>> document here:
> >>>>> https://docs.galaxyproject.org/en/master/admin/conda_faq.html
> >>>>>
> >>>>> Best,
> >>>>> Marius
> >>>>>
> >>>>> On 18 April 2017 at 19:03, Matthias Bernt <m.be...@ufz.de
> >>>>> <mailto:m.be...@ufz.de>> wrote:
> >>>>>
> >>>>>     Dear list,
> >>>>>
> >>>>>     again me :( stumbling from problem to problem ...
> >>>>>
> >>>>>     I got compilation errors when installing
> >>>>>
> >>>>>     package_atlas_3_10 Revision: 98c017ec230d
> >>>>>
> >>>>>     I tried with gcc 4x and 6x without success. Do I need the intel C
> >>>>>     compiler for this tool?
> >>>>>
> >>>>>     If I got earlier posts
> >>>>>
> >>>>> (
> http://dev.list.galaxyproject.org/atlas-3-10-IUC-error-tt4668236.html
> >>>>>
> >>>>> <
> http://dev.list.galaxyproject.org/atlas-3-10-IUC-error-tt4668236.html>)
> >>>>>
> >>>>>     correct a precompiled version should be used anyway?
> >>>>>
> >>>>>     I'm running galaxy on CentOS 6.8 (64bit) (running in a
> VirtualBox).
> >>>>>
> >>>>>     Best,
> >>>>>     Matthias
> >>>>>
> >>>>>
> >>>>>     Here is the output (which I guess is verbose output from
> configure):
> >>>>>
> >>>>>
> >>>>>     /tmp/cctyMGAH.o: In function `ATL_tmpnam':
> >>>>>
> >>>>>
> >>>>>
> /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
> >>>>>     warning: the use of `tmpnam' is dangerous, better use `mkstemp'
> >>>>>     probe_OS.o: In function `ATL_tmpnam':
> >>>>>
> >>>>>
> >>>>>
> /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
> >>>>>     warning: the use of `tmpnam' is dangerous, better use `mkstemp'
> >>>>>     probe_asm.o: In function `ATL_tmpnam':
> >>>>>
> >>>>>
> >>>>>
> /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
> >>>>>     warning: the use of `tmpnam' is dangerous, better use `mkstemp'
> >>>>>     system(make IRun_GAS_x8632 args="-v 2" MYFLAGS="-DATL_OS_Linux"
> 2>
> >>>>>     /dev/null | fgrep SUCCESS)
> >>>>>
> >>>>>     ierr=256 in command='make IRun_GAS_x8632 args="-v 2"
> >>>>>     MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS'!
> >>>>>
> >>>>>     OUTPUT:
> >>>>>     =======
> >>>>>     system(make IRun_GAS_x8664 args="-v 2" MYFLAGS="-DATL_OS_Linux"
> 2>
> >>>>>     /dev/null | fgrep SUCCESS)
> >>>>>     probe_vec.o: In function `ATL_tmpnam':
> >>>>>
> >>>>>
> >>>>>
> /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
> >>>>>     warning: the use of `tmpnam' is dangerous, better use `mkstemp'
> >>>>>
> >>>>>     ierr=256 in command='make IRun_VSX MYFLAGS='-DATL_OS_Linux
> >>>>>     -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!
> >>>>>
> >>>>>     OUTPUT:
> >>>>>     =======
> >>>>>
> >>>>>     ierr=256 in command='make IRun_AltiVec MYFLAGS='-DATL_OS_Linux
> >>>>>     -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!
> >>>>>
> >>>>>     OUTPUT:
> >>>>>     =======
> >>>>>
> >>>>>     ierr=256 in command='make IRun_AVXFMA4 MYFLAGS='-DATL_OS_Linux
> >>>>>     -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!
> >>>>>
> >>>>>     OUTPUT:
> >>>>>     =======
> >>>>>
> >>>>>     ierr=256 in command='make IRun_3DNow MYFLAGS='-DATL_OS_Linux
> >>>>>     -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!
> >>>>>
> >>>>>     OUTPUT:
> >>>>>     =======
> >>>>>
> >>>>>     ierr=256 in command='make IRun_NEON MYFLAGS='-DATL_OS_Linux
> >>>>>     -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!
> >>>>>
> >>>>>     OUTPUT:
> >>>>>     =======
> >>>>>     probe_arch.o: In function `ATL_tmpnam':
> >>>>>
> >>>>>
> >>>>>
> /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
> >>>>>     warning: the use of `tmpnam' is dangerous, better use `mkstemp'
> >>>>>     /tmp/cc8hbxc1.o: In function `ATL_tmpnam':
> >>>>>
> >>>>>
> >>>>>
> /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
> >>>>>     warning: the use of `tmpnam' is dangerous, better use `mkstemp'
> >>>>>     ERROR: enum fam=3, chip=2, model=79, mach=0
> >>>>>     make[3]: *** [atlas_run] Error 44
> >>>>>     make[2]: *** [IRunArchInfo_x86] Error 2
> >>>>>     /tmp/ccafA8Bi.o: In function `ATL_tmpnam':
> >>>>>
> >>>>>
> >>>>>
> /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
> >>>>>     warning: the use of `tmpnam' is dangerous, better use `mkstemp'
> >>>>>     ERROR: enum fam=3, chip=2, model=79, mach=0
> >>>>>     make[3]: *** [atlas_run] Error 44
> >>>>>     make[2]: *** [IRunArchInfo_x86] Error 2
> >>>>>     ERROR: enum fam=3, chip=2, model=79, mach=0
> >>>>>     make[3]: *** [atlas_run] Error 44
> >>>>>     make[2]: *** [IRunArchInfo_x86] Error 2
> >>>>>     cmnd='make IRun_comp args="-v 2 -o atlconf.txt -O 1 -A 39 -Si
> nof77
> >>>>>     0 -V 488  -Fa ic '-fPIC' -Fa sm '-fPIC' -Fa dm '-fPIC' -Fa sk
> >>>>>     '-fPIC' -Fa dk '-fPIC' -Fa xc '-fPIC' -Fa gc '-fPIC' -Fa if
> '-fPIC'
> >>>>>     -b 64"'
> >>>>>     /tmp/cc8W8Itx.o: In function `ATL_tmpnam':
> >>>>>
> >>>>>
> >>>>>
> /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
> >>>>>     warning: the use of `tmpnam' is dangerous, better use `mkstemp'
> >>>>>     probe_comp.o: In function `ATL_tmpnam':
> >>>>>
> >>>>>
> >>>>>
> /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224:
> >>>>>     warning: the use of `tmpnam' is dangerous, better use `mkstemp'
> >>>>>
> >>>>>     ierr=256 in command='find
> >>>>>     /gpfs1/data/galaxy_server/galaxy-dev/.venv/bin
> >>>>>     /usr/local/gcc/6.2.0-1/bin
> >>>>>     /global/apps/bioinf/galaxy/bin/Python-2.7.13/bin
> >>>>>     /usr/local/sqlite/3.15.1-1/bin
> >>>>>     /global/apps/bioinf/galaxy/bin/postgresql-9.6.2/bin
> >>>>>     /usr/local/git/2.10.1-1/bin /usr/local/pcre/8.38-1/bin
> >>>>>     /usr/local/ncurses/5.9-1/bin /usr/local/bzip2/1.0.6-3/bin
> >>>>>     /usr/local/expat/2.1.1-1/bin /usr/local/curl/7.41.0-1/bin
> >>>>>     /usr/local/openssl/1.0.2-1/usr/bin
> >>>>>     /usr/local/uge/8.4.4-1/bin/lx-amd64 /usr/local/bin /bin /usr/bin
> >>>>>     /usr/local/sbin /usr/sbin /sbin /home/songalax/bin -maxdepth 1
> -name
> >>>>>     '*gcc*' -exec ./xisgcc '{}' \;'!
> >>>>>
> >>>>>     OUTPUT:
> >>>>>     =======
> >>>>>     cmnd=make IRunCComp CC='/usr/local/gcc/6.2.0-1/bin/gcc'
> >>>>>     CCFLAGS='-O'  | fgrep SUCCESS
> >>>>>        /usr/local/gcc/6.2.0-1/bin/gcc -O : SUCCESS!
> >>>>>     cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O'  | fgrep
> SUCCESS
> >>>>>        /usr/bin/gcc -O : SUCCESS!
> >>>>>     sh: -c: line 0: unexpected EOF while looking for matching ``'
> >>>>>     sh: -c: line 1: syntax error: unexpected end of file
> >>>>>
> >>>>>     ierr=256 in command='find $HOME/local -name '*gcc*' -exec
> ./xisgcc
> >>>>>     '{}' \;'!
> >>>>>
> >>>>>     OUTPUT:
> >>>>>     =======
> >>>>>     cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O'  | fgrep
> SUCCESS
> >>>>>        /usr/bin/gcc -O : SUCCESS!
> >>>>>     sh: -c: line 0: unexpected EOF while looking for matching ``'
> >>>>>     sh: -c: line 1: syntax error: unexpected end of file
> >>>>>
> >>>>>     ierr=256 in command='find /usr/local /bin /sbin /usr/bin
> /usr/sbin
> >>>>>     /opt/bin /opt/sbin -name '*gcc*' -exec ./xisgcc '{}' \;'!
> >>>>>
> >>>>>     OUTPUT:
> >>>>>     =======
> >>>>>     cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O'  | fgrep
> SUCCESS
> >>>>>        /usr/bin/gcc -O : SUCCESS!
> >>>>>     sh: -c: line 0: unexpected EOF while looking for matching ``'
> >>>>>     sh: -c: line 1: syntax error: unexpected end of file
> >>>>>     sh: -c: line 0: unexpected EOF while looking for matching ``'
> >>>>>     sh: -c: line 1: syntax error: unexpected end of file
> >>>>>
> >>>>>     Compiler nodes: Fresh Read
> >>>>>       0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77'
> >>>>>          '-O'
> >>>>>       1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77'
> >>>>>          '-O'
> >>>>>       2. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran'
> >>>>>          '-O'
> >>>>>       3. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc'
> >>>>>          '-O -fomit-frame-pointer'
> >>>>>       4. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran'
> >>>>>          '-mcpu=cortex-a8 -mfpu=vfpv3 -mfloat-abi=softfp -O'
> >>>>>       5. priority=1000, comps,OS,arch[0]=(20,1,0), comp='gcc'
> >>>>>          '-O1 -mcpu=cortex-a8 -mtune=cortex-a8 -mfpu=vfpv3
> >>>>>     -mfloat-abi=softfp -fno-schedule-insns2'
> >>>>>       6. priority=1000, comps,OS,arch[0]=(75,1,0), comp='gcc'
> >>>>>          '-O1 -mcpu=cortex-a8 -mtune=cortex-a8 -mfpu=vfpv3
> >>>>>     -mfloat-abi=softfp -fno-expensive-optimizations'
> >>>>>       7. priority=1000, comps,OS,arch[0]=(32,1,0), comp='gcc'
> >>>>>          '-mcpu=cortex-a8 -O1 -mfpu=vfpv3 -mfloat-abi=softfp '
> >>>>>       8. priority=0, comps,OS,arch[0]=(63,768,1075838976), comp='icl'
> >>>>>          '-QxN -O3 -Qprec -fp:extended -fp:except -nologo -Oy'
> >>>>>       9. priority=0, comps,OS,arch[0]=(128,768,1), comp='ifort'
> >>>>>          '-O2 -fltconsistency -nologo'
> >>>>>      10. priority=0, comps,OS,arch[0]=(63,768,1), comp='cl'
> >>>>>          '-Oy -Ox -arch:SSE2 -nologo'
> >>>>>      11. priority=4, comps,OS,arch[0]=(63,768,1048576), comp='cl'
> >>>>>          '-Oy -Ox -arch:SSE -nologo'
> >>>>>      12. priority=4, comps,OS,arch[0]=(63,768,983040), comp='cl'
> >>>>>          '-Oy -Ox'
> >>>>>      13. priority=500, comps,OS,arch[0]=(127,1,3584), comp='gcc'
> >>>>>          '-O3 -funroll-loops'
> >>>>>      14. priority=500, comps,OS,arch[0]=(128,1,3584), comp='gfortran'
> >>>>>          '-O3 -funroll-loops'
> >>>>>      15. priority=600, comps,OS,arch[0]=(128,1,2048), comp='gfortran'
> >>>>>          '-march=z9-109 -O3 -funroll-loops'
> >>>>>      16. priority=600, comps,OS,arch[0]=(127,1,2048), comp='gcc'
> >>>>>          '-march=z9-109 -O3 -funroll-loops'
> >>>>>      17. priority=800, comps,OS,arch[0]=(128,1,2048), comp='gfortran'
> >>>>>          '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays'
> >>>>>      18. priority=800, comps,OS,arch[0]=(127,1,2048), comp='gcc'
> >>>>>          '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays'
> >>>>>      19. priority=1000, comps,OS,arch[0]=(127,1,2048), comp='gcc'
> >>>>>          '-march=z196 -O3 -funroll-loops -fno-prefetch-loop-arrays'
> >>>>>      20. priority=1000, comps,OS,arch[0]=(128,1,2048),
> comp='gfortran'
> >>>>>          '-march=z196 -O3 -funroll-loops -fno-prefetch-loop-arrays'
> >>>>>      21. priority=600, comps,OS,arch[0]=(127,1,1024), comp='gcc'
> >>>>>          '-march=z9-109 -O3 -funroll-loops -fno-prefetch-loop-arrays'
> >>>>>      22. priority=600, comps,OS,arch[0]=(128,1,1024), comp='gfortran'
> >>>>>          '-march=z9-109 -O3 -funroll-loops'
> >>>>>      23. priority=1000, comps,OS,arch[0]=(127,1,1024), comp='gcc'
> >>>>>          '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays'
> >>>>>      24. priority=1000, comps,OS,arch[0]=(127,1,512), comp='gcc'
> >>>>>          '-march=z9-109 -O3 -funroll-loops'
> >>>>>      25. priority=1010, comps,OS,arch[0]=(128,1,4), comp='xlf'
> >>>>>          '-qtune=pwr4 -qarch=pwr4 -O3 -qmaxmem=-1 -qfloat=hsflt'
> >>>>>      26. priority=1010, comps,OS,arch[0]=(127,1,4), comp='gcc'
> >>>>>          '-mcpu=power4 -mtune=power4 -O3 -fno-schedule-insns
> >>>>>     -fno-rerun-loop-opt'
> >>>>>      27. priority=1010, comps,OS,arch[0]=(128,1,8), comp='xlf'
> >>>>>          '-qtune=pwr5 -qarch=pwr5 -O3 -qmaxmem=-1 -qfloat=hsflt'
> >>>>>      28. priority=1010, comps,OS,arch[0]=(128,1,128), comp='xlf'
> >>>>>          '-qtune=pwr7 -qarch=pwr7 -O3 -qmaxmem=-1 -qfloat=hsflt'
> >>>>>      29. priority=1010, comps,OS,arch[0]=(128,1,8), comp='gfortran'
> >>>>>          '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns
> >>>>>     -fno-rerun-loop-opt'
> >>>>>      30. priority=1010, comps,OS,arch[0]=(128,1,64), comp='gfortran'
> >>>>>          '-mcpu=power6 -mtune=power6 -maltivec -O3
> -fno-schedule-insns
> >>>>>     -fschedule-insns2 -minsert-sched-nops=2'
> >>>>>      31. priority=1010, comps,OS,arch[0]=(127,1,8), comp='gcc'
> >>>>>          '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns
> >>>>>     -fno-rerun-loop-opt'
> >>>>>      32. priority=1010, comps,OS,arch[0]=(127,1,64), comp='gcc'
> >>>>>          '-mcpu=power6 -mtune=power6 -maltivec -O3
> -fno-schedule-insns
> >>>>>     -fschedule-insns2 -minsert-sched-nops=2'
> >>>>>      33. priority=1010, comps,OS,arch[0]=(128,1,128), comp='gfortran'
> >>>>>          '-O2 -mvsx -mcpu=power7 -mtune=power7 -m64 -mvrsave
> >>>>>     -funroll-all-loops'
> >>>>>      34. priority=1010, comps,OS,arch[0]=(127,1,128), comp='gcc'
> >>>>>          '-O2 -mvsx -mcpu=power7 -mtune=power7 -m64 -mvrsave
> >>>>>     -funroll-all-loops'
> >>>>>      35. priority=1000, comps,OS,arch[0]=(8,1,32), comp='gcc'
> >>>>>          '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970
> -O2
> >>>>>     -mvrsave'
> >>>>>      36. priority=1000, comps,OS,arch[0]=(117,1,32), comp='gcc'
> >>>>>          '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970
> -O2'
> >>>>>      37. priority=1000, comps,OS,arch[0]=(2,1,32), comp='gcc'
> >>>>>          '-Os -mpowerpc64 -maltivec -mabi=altivec -mcpu=970
> -mtune=970
> >>>>>     -mvrsave -fno-schedule-insns2 -fno-schedule-insns'
> >>>>>      38. priority=1000, comps,OS,arch[0]=(121,1,16), comp='gcc'
> >>>>>          '-O3 -maltivec -mabi=altivec -mcpu=7400 -mtune=7400
> >>>>>     -fno-schedule-insns -fschedule-insns2'
> >>>>>      39. priority=1000, comps,OS,arch[0]=(2,1,16), comp='gcc'
> >>>>>          '-Os -maltivec -mabi=altivec -mcpu=7400 -mtune=7400'
> >>>>>      40. priority=1000, comps,OS,arch[0]=(4,1,16), comp='gcc'
> >>>>>          '-Os -maltivec -mabi=altivec -mcpu=7400 -mtune=7400'
> >>>>>      41. priority=1, comps,OS,arch[0]=(33,1,0), comp='pathcc'
> >>>>>          '-march=auto -O2 -OPT:Olimit=15000 -LNO:blocking=OFF'
> >>>>>      42. priority=1, comps,OS,arch[0]=(6,1,0), comp='pathcc'
> >>>>>          '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed
> >>>>>     -march=auto -LNO:opt=0 -LNO:full_unroll_outer=OFF -LNO:fusion=0
> >>>>>     -LNO:prefetch=2'
> >>>>>      43. priority=1, comps,OS,arch[0]=(24,1,0), comp='pathcc'
> >>>>>          '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed
> >>>>>     -march=auto'
> >>>>>      44. priority=1000, comps,OS,arch[0]=(128,1,0), comp='pathf95'
> >>>>>          '-march=auto -O2'
> >>>>>      45. priority=500, comps,OS,arch[0]=(127,1,0), comp='gcc'
> >>>>>          '-O2 -mips64 -march=5kf -mtune=5kf -fno-schedule-insns
> >>>>>     -fschedule-insns2 -fno-peephole -fno-peephole2'
> >>>>>      46. priority=1000, comps,OS,arch[0]=(128,32,0), comp='f77'
> >>>>>          '-O2'
> >>>>>      47. priority=1000, comps,OS,arch[0]=(97,32,0), comp='cc'
> >>>>>          '-O2 -OPT:Olimit=15000 -LNO:blocking=OFF'
> >>>>>      48. priority=1000, comps,OS,arch[0]=(30,32,0), comp='cc'
> >>>>>          '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed'
> >>>>>      49. priority=1010, comps,OS,arch[0]=(128,1,0), comp='gfortran'
> >>>>>          '-fomit-frame-pointer -O2 -fno-tree-loop-optimize'
> >>>>>      50. priority=1000, comps,OS,arch[0]=(30,1,0), comp='gcc'
> >>>>>          '-fomit-frame-pointer -O2'
> >>>>>      51. priority=1010, comps,OS,arch[0]=(30,1,0), comp='gcc'
> >>>>>          '-fomit-frame-pointer -O2 -fno-tree-loop-optimize'
> >>>>>      52. priority=10, comps,OS,arch[0]=(128,1,0), comp='g77'
> >>>>>          '-O -mcpu=ultrasparc3 -mtune=ultrasparc3'
> >>>>>      53. priority=100, comps,OS,arch[0]=(128,1,0), comp='gfortran'
> >>>>>          '-O -mcpu=ultrasparc3 -mtune=ultrasparc3'
> >>>>>      54. priority=1000, comps,OS,arch[0]=(128,1,0), comp='f77'
> >>>>>          '-dalign -native -xO5'
> >>>>>      55. priority=1000, comps,OS,arch[0]=(96,1,0), comp='gcc'
> >>>>>          '-mcpu=ultrasparc3 -mtune=ultrasparc3 -O'
> >>>>>      56. priority=1000, comps,OS,arch[0]=(29,1,0), comp='gcc'
> >>>>>          '-O3 -mcpu=ultrasparc3 -mtune=ultrasparc3
> -fno-schedule-insns2
> >>>>>     -fschedule-insns'
> >>>>>      57. priority=1000, comps,OS,arch[0]=(2,1,0), comp='gcc'
> >>>>>          '-O1 -mcpu=ultrasparc3 -mtune=ultrasparc3 -fschedule-insns
> >>>>>     -fmodulo-sched'
> >>>>>      58. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran'
> >>>>>          '-mcpu=niagara2 -mtune=niagara2 -Os'
> >>>>>      59. priority=1000, comps,OS,arch[0]=(127,1,0), comp='gcc'
> >>>>>          '-mcpu=niagara2 -mtune=niagara2 -Os'
> >>>>>      60. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc'
> >>>>>          '-fomit-frame-pointer -mfpmath=sse -mfma4 -O2
> >>>>>     -fno-tree-loop-optimize'
> >>>>>      61. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc'
> >>>>>          '-Os -fomit-frame-pointer'
> >>>>>      62. priority=1005, comps,OS,arch[0]=(95,896,0), comp='gcc'
> >>>>>          '-fomit-frame-pointer -mfpmath=sse -O2'
> >>>>>      63. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc'
> >>>>>          '-fomit-frame-pointer -mfpmath=sse -O2'
> >>>>>      64. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran'
> >>>>>          '-fomit-frame-pointer -mfpmath=sse -O2'
> >>>>>      65. priority=1000, comps,OS,arch[0]=(95,1,12582912), comp='gcc'
> >>>>>          '-fomit-frame-pointer -O3 -mfpmath=387'
> >>>>>      66. priority=1005, comps,OS,arch[0]=(31,896,12582912),
> comp='gcc-4'
> >>>>>          '-fomit-frame-pointer -O3 -mfpmath=387'
> >>>>>      67. priority=1000, comps,OS,arch[0]=(95,1,-1071906816),
> comp='gcc'
> >>>>>          '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
> >>>>>      68. priority=1005, comps,OS,arch[0]=(31,896,1835008),
> comp='gcc-4'
> >>>>>          '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
> >>>>>      69. priority=1000, comps,OS,arch[0]=(128,1,1835008),
> >>>>> comp='gfortran'
> >>>>>          '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
> >>>>>      70. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc'
> >>>>>          '-fomit-frame-pointer -mfpmath=387 -O2'
> >>>>>      71. priority=1005, comps,OS,arch[0]=(31,896,0), comp='gcc-4'
> >>>>>          '-fomit-frame-pointer -mfpmath=387 -O2'
> >>>>>      72. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran'
> >>>>>          '-fomit-frame-pointer -mfpmath=387 -O2'
> >>>>>      73. priority=1000, comps,OS,arch[0]=(25,1,-1073741824),
> >>>>> comp='gcc-4'
> >>>>>          '-O2 -fomit-frame-pointer -mfpmath=sse'
> >>>>>      74. priority=1005, comps,OS,arch[0]=(6,896,-1073741824),
> >>>>> comp='gcc-4'
> >>>>>          '-O2 -fomit-frame-pointer -mfpmath=sse -fno-schedule-insns
> >>>>>     -fno-optimize-register-move'
> >>>>>      75. priority=1000, comps,OS,arch[0]=(6,1,-1073741824),
> comp='gcc'
> >>>>>          '-O2 -fomit-frame-pointer -mfpmath=sse -fno-schedule-insns
> >>>>>     -fno-optimize-register-move'
> >>>>>      76. priority=1000, comps,OS,arch[0]=(25,1,-2147483648),
> comp='gcc'
> >>>>>          '-O2 -fomit-frame-pointer -mfpmath=sse'
> >>>>>      77. priority=1000, comps,OS,arch[0]=(128,1,-1073741824),
> >>>>>     comp='gfortran'
> >>>>>          '-O2 -fomit-frame-pointer -mfpmath=sse'
> >>>>>      78. priority=1000, comps,OS,arch[0]=(128,1,32768),
> comp='gfortran'
> >>>>>          '-fomit-frame-pointer -mfpmath=sse -O2'
> >>>>>      79. priority=1000, comps,OS,arch[0]=(95,1,32768), comp='gcc'
> >>>>>          '-fomit-frame-pointer -mfpmath=sse -O2'
> >>>>>      80. priority=1000, comps,OS,arch[0]=(128,1,16384),
> comp='gfortran'
> >>>>>          '-fomit-frame-pointer -mfpmath=sse -O2'
> >>>>>      81. priority=1000, comps,OS,arch[0]=(95,1,16384), comp='gcc'
> >>>>>          '-fomit-frame-pointer -mfpmath=sse -O2'
> >>>>>      82. priority=1000, comps,OS,arch[0]=(128,1,8192),
> comp='gfortran'
> >>>>>          '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
> >>>>>      83. priority=1000, comps,OS,arch[0]=(10,1,8192), comp='gcc'
> >>>>>          '-fomit-frame-pointer -mfpmath=sse -O2'
> >>>>>      84. priority=1000, comps,OS,arch[0]=(85,1,8192), comp='gcc'
> >>>>>          '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
> >>>>>      85. priority=1000, comps,OS,arch[0]=(128,1,12288),
> comp='gfortran'
> >>>>>          '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
> >>>>>      86. priority=1000, comps,OS,arch[0]=(95,1,4096), comp='gcc'
> >>>>>          '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4'
> >>>>>      87. priority=1000, comps,OS,arch[0]=(65,1,536870912), comp='gcc'
> >>>>>          '-O'
> >>>>>      88. priority=1000, comps,OS,arch[0]=(30,1,536870912), comp='gcc'
> >>>>>          '-O3 -fno-schedule-insns2 -funroll-all-loops -fno-tree-ch'
> >>>>>      89. priority=1000, comps,OS,arch[0]=(95,1,33554432), comp='gcc'
> >>>>>          '-fomit-frame-pointer -mfpmath=sse -O2'
> >>>>>      90. priority=1005, comps,OS,arch[0]=(31,896,33554432),
> comp='gcc-4'
> >>>>>          '-fomit-frame-pointer -mfpmath=sse -O2'
> >>>>>      91. priority=1000, comps,OS,arch[0]=(95,1,67108864), comp='gcc'
> >>>>>          '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2'
> >>>>>      92. priority=1005, comps,OS,arch[0]=(95,896,67108864),
> comp='gcc-4'
> >>>>>          '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2'
> >>>>>      93. priority=50, comps,OS,arch[0]=(57,1,134217728), comp='clang'
> >>>>>          '-fomit-frame-pointer -mavx -O2 -m64 -Wno-parentheses'
> >>>>>      94. priority=1000, comps,OS,arch[0]=(127,1,134217728),
> comp='gcc'
> >>>>>          '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2'
> >>>>>      95. priority=1005, comps,OS,arch[0]=(31,896,134217728),
> >>>>> comp='gcc-4'
> >>>>>          '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2'
> >>>>>      96. priority=1000, comps,OS,arch[0]=(127,1,268435456),
> comp='gcc'
> >>>>>          '-fomit-frame-pointer -mfpmath=sse -O2'
> >>>>>
> >>>>>
> >>>>>     Compiler nodes: Targeted
> >>>>>       0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77'
> >>>>>          '-O'
> >>>>>       1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77'
> >>>>>          '-O'
> >>>>>       2. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran'
> >>>>>          '-O'
> >>>>>       3. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc'
> >>>>>          '-O -fomit-frame-pointer'
> >>>>>
> >>>>>
> >>>>>     Compiler nodes: Sorted
> >>>>>       0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77'
> >>>>>          '-O'
> >>>>>       1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77'
> >>>>>          '-O'
> >>>>>       2. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc'
> >>>>>          '-O -fomit-frame-pointer'
> >>>>>       3. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran'
> >>>>>          '-O'
> >>>>>
> >>>>>     cc1: error: unrecognized command line option "-mavx2"
> >>>>>     make[2]: *** [IRunCComp] Error 1
> >>>>>
> >>>>>     ierr=256 in command='make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O
> >>>>>     -fomit-frame-pointer -mavx2 -mfma -fPIC -m64'  | fgrep SUCCESS'!
> >>>>>
> >>>>>     OUTPUT:
> >>>>>     =======
> >>>>>     cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O
> >>>>>     -fomit-frame-pointer -mavx2 -mfma -fPIC -m64'  | fgrep SUCCESS
> >>>>>        /usr/bin/gcc -O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64 :
> >>>>>     FAILURE!
> >>>>>
> >>>>>
> >>>>>     Unable to find usable compiler for ICC; abortingMake sure
> compilers
> >>>>>     are in your path, and specify good compilers to configure
> >>>>>     (see INSTALL.txt or 'configure --help' for details)make[1]: ***
> >>>>>     [atlas_run] Error 1
> >>>>>     make: *** [IRun_comp] Error 2
> >>>>>     ERROR 512 IN SYSCMND: 'make IRun_comp args="-v 2 -o atlconf.txt
> -O 1
> >>>>>     -A 39 -Si nof77 0 -V 488  -Fa ic '-fPIC' -Fa sm '-fPIC' -Fa dm
> >>>>>     '-fPIC' -Fa sk '-fPIC' -Fa dk '-fPIC' -Fa xc '-fPIC' -Fa gc
> '-fPIC'
> >>>>>     -Fa if '-fPIC' -b 64"'
> >>>>>     Make.top:1: Make.inc: No such file or directory
> >>>>>     Make.top:329: warning: overriding commands for target
> `/AtlasTest'
> >>>>>     Make.top:80: warning: ignoring old commands for target
> `/AtlasTest'
> >>>>>     make[1]: *** No rule to make target `Make.inc'.  Stop.
> >>>>>     make: *** [startup] Error 2
> >>>>>     mv: cannot stat `lib/Makefile': No such file or directory
> >>>>>     ../configure: line 450: lib/Makefile: No such file or directory
> >>>>>     ../configure: line 451: lib/Makefile: No such file or directory
> >>>>>     ../configure: line 452: lib/Makefile: No such file or directory
> >>>>>     ../configure: line 453: lib/Makefile: No such file or directory
> >>>>>     ../configure: line 509: lib/Makefile: No such file or directory
> >>>>>     Make.top:1: Make.inc: No such file or directory
> >>>>>     Make.top:329: warning: overriding commands for target
> `/AtlasTest'
> >>>>>     Make.top:80: warning: ignoring old commands for target
> `/AtlasTest'
> >>>>>     make[1]: *** No rule to make target `Make.inc'.  Stop.
> >>>>>     make: *** [build] Error 2
> >>>>>     --
> >>>>>
> >>>>>     -------------------------------------------
> >>>>>     Matthias Bernt
> >>>>>     Bioinformatics Service
> >>>>>     Molekulare Systembiologie (MOLSYB)
> >>>>>     Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> >>>>>     Helmholtz Centre for Environmental Research GmbH - UFZ
> >>>>>     Permoserstraße 15, 04318 Leipzig, Germany
> >>>>>     Phone +49 341 235 482296 <tel:%2B49%20341%20235%20482296>,
> >>>>>     m.be...@ufz.de <mailto:m.be...@ufz.de>, www.ufz.de
> >>>>> <http://www.ufz.de>
> >>>>>
> >>>>>     Sitz der Gesellschaft/Registered Office: Leipzig
> >>>>>     Registergericht/Registration Office: Amtsgericht Leipzig
> >>>>>     Handelsregister Nr./Trade Register Nr.: B 4703
> >>>>>     Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
> >>>>>     MinDirig Wilfried Kraus
> >>>>>     Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
> >>>>>     Prof. Dr. Dr. h.c. Georg Teutsch
> >>>>>     Administrative Geschäftsführerin/ Administrative Managing
> Director:
> >>>>>     Prof. Dr. Heike Graßmann
> >>>>>     -------------------------------------------
> >>>>>
> >>>>>
> >>>>>     ___________________________________________________________
> >>>>>     Please keep all replies on the list by using "reply all"
> >>>>>     in your mail client.  To manage your subscriptions to this
> >>>>>     and other Galaxy lists, please use the interface at:
> >>>>>       https://lists.galaxyproject.org/
> >>>>> <https://lists.galaxyproject.org/>
> >>>>>
> >>>>>     To search Galaxy mailing lists use the unified search at:
> >>>>>       http://galaxyproject.org/search/
> >>>>> <http://galaxyproject.org/search/>
> >>>>>
> >>>>>
> >>>>
> >>>> --
> >>>>
> >>>> -------------------------------------------
> >>>> Matthias Bernt
> >>>> Bioinformatics Service
> >>>> Molekulare Systembiologie (MOLSYB)
> >>>> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> >>>> Helmholtz Centre for Environmental Research GmbH - UFZ
> >>>> Permoserstraße 15, 04318 Leipzig, Germany
> >>>> Phone +49 341 235 482296,
> >>>> m.be...@ufz.de, www.ufz.de
> >>>>
> >>>> Sitz der Gesellschaft/Registered Office: Leipzig
> >>>> Registergericht/Registration Office: Amtsgericht Leipzig
> >>>> Handelsregister Nr./Trade Register Nr.: B 4703
> >>>> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
> >>>> MinDirig
> >>>> Wilfried Kraus
> >>>> Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
> >>>> Prof. Dr. Dr. h.c. Georg Teutsch
> >>>> Administrative Geschäftsführerin/ Administrative Managing Director:
> >>>> Prof. Dr. Heike Graßmann
> >>>> -------------------------------------------
> >>>>
> >>>>
> >>>> ___________________________________________________________
> >>>> Please keep all replies on the list by using "reply all"
> >>>> in your mail client.  To manage your subscriptions to this
> >>>> and other Galaxy lists, please use the interface at:
> >>>>   https://lists.galaxyproject.org/
> >>>>
> >>>> To search Galaxy mailing lists use the unified search at:
> >>>>   http://galaxyproject.org/search/
> >>
> >>
> >> --
> >>
> >> -------------------------------------------
> >> Matthias Bernt
> >> Bioinformatics Service
> >> Molekulare Systembiologie (MOLSYB)
> >> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> >> Helmholtz Centre for Environmental Research GmbH - UFZ
> >> Permoserstraße 15, 04318 Leipzig, Germany
> >> Phone +49 341 235 482296,
> >> m.be...@ufz.de, www.ufz.de
> >>
> >> Sitz der Gesellschaft/Registered Office: Leipzig
> >> Registergericht/Registration Office: Amtsgericht Leipzig
> >> Handelsregister Nr./Trade Register Nr.: B 4703
> >> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
> MinDirig
> >> Wilfried Kraus
> >> Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
> >> Prof. Dr. Dr. h.c. Georg Teutsch
> >> Administrative Geschäftsführerin/ Administrative Managing Director:
> >> Prof. Dr. Heike Graßmann
> >> -------------------------------------------
> >>
>
> --
>
> -------------------------------------------
> Matthias Bernt
> Bioinformatics Service
> Molekulare Systembiologie (MOLSYB)
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> Helmholtz Centre for Environmental Research GmbH - UFZ
> Permoserstraße 15, 04318 Leipzig, Germany
> Phone +49 341 235 482296,
> m.be...@ufz.de, www.ufz.de
>
> Sitz der Gesellschaft/Registered Office: Leipzig
> Registergericht/Registration Office: Amtsgericht Leipzig
> Handelsregister Nr./Trade Register Nr.: B 4703
> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
> MinDirig Wilfried Kraus
> Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
> Prof. Dr. Dr. h.c. Georg Teutsch
> Administrative Geschäftsführerin/ Administrative Managing Director:
> Prof. Dr. Heike Graßmann
> -------------------------------------------
>
>
___________________________________________________________
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