Re: [ModPipe-users] [modeller_usage] Fwd: Installation Issues
On 10/18/2013 01:12 PM, Amjad Farooq wrote: > However, when I run a test under /tests, I get the following error: > > make > ************************************************************************** > cd unit && ../../int/runscript.sh python run-all-tests.py -v > /dev/null > /bin/sh: ../../int/runscript.sh: No such file or directory > make: *** [unit] Error 127 > ************************************************************************** > > Where is this ../../int/runscript.sh script? The /int directory is empty!
It looks like you forgot to run the Setup script.
Ben Webb, Modeller Caretaker
Ben,
You are right. I forgot to run: > ./Setup --with-cd-hit=no --with-blast=no --with-spasm=no --with-procheck=no
since I have installed none of the external packages but modeller9.12.
However, when I run the demo under /demo, I get this error: > python AddSeqMP.py --conf_file modpipe.conf --sequence_file test.fsa
************************************************************************** Traceback (most recent call last): File "AddSeqMP.py", line 17, in <module> import modpipe.version ImportError: No module named modpipe.version **************************************************************************
How do I fix this?
Amjad
On Fri, Oct 18, 2013 at 4:21 PM, Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 10/18/2013 01:12 PM, Amjad Farooq wrote: > >> However, when I run a test under /tests, I get the following error: >> > make >> **************************************************************** >> ************** >> cd unit && ../../int/runscript.sh python run-all-tests.py -v > /dev/null >> /bin/sh: ../../int/runscript.sh: No such file or directory >> make: *** [unit] Error 127 >> **************************************************************** >> ************** >> >> Where is this ../../int/runscript.sh script? The /int directory is empty! >> > > It looks like you forgot to run the Setup script. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/**modeller/http://www.salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/**listinfo/modeller_usagehttps://salilab.org/mailman/listinfo/modeller_usage >
On 10/18/2013 02:28 PM, Amjad Farooq wrote: > ImportError: No module named modpipe.version
This file should also be generated by Setup, so it suggests that Setup didn't run properly. Does $MODPIPE/lib/python/modpipe/version.py exist?
Ben
Yes, ./lib/python/modpipe/version.py exists:
> more ./lib/python/modpipe/version.py
****************************************************************************** # This file is part of ModPipe, Copyright 1997-2010 Andrej Sali # # ModPipe is free software: you can redistribute it and/or modify # it under the terms of version 2 of the GNU General Public License # as published by the Free Software Foundation. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with ModPipe. If not, see http://www.gnu.org/licenses/.
def get(): return "2.2.0"
def message(): return "%prog, part of ModPipe version " + get() + """ Copyright 1997-2010 Andrej Sali License GPLv2: GNU GPL version 2 http://gnu.org/licenses/gpl.html This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.""" ******************************************************************************
But, may be this would help: When I run a test, I get these errors:
> ./tests/make
====================================================================== ERROR: test_ce (test_ce.CETests) Check CE ---------------------------------------------------------------------- Traceback (most recent call last): File "/alpha/share/software/bioinf/MODPIPE/modpipe220/tests/unit/test_ce.py", line 12, in test_ce ce = modpipe.binaries.get_ce() File "/alpha/share/software/bioinf/MODPIPE/modpipe220/lib/python/modpipe/binaries.py", line 45, in get_ce raise modpipe.MissingBinaryError('ModPipe was not configured with CE') MissingBinaryError: ModPipe was not configured with CE
====================================================================== FAIL: test_make_one_file (test_make_chains.MakeChainsTests) Check production of one aggregated chains file ---------------------------------------------------------------------- Traceback (most recent call last): File "/alpha/share/software/bioinf/MODPIPE/modpipe220/tests/unit/test_make_chains.py", line 52, in test_make_one_file self.assert_(filecmp.cmp(out, '../db/test-pdb.pir')) AssertionError: False is not True
---------------------------------------------------------------------- Ran 51 tests in 6.151s
FAILED (failures=1, errors=8) make: *** [unit] Error 1 ----------------------------------------------------------------------
Thanks for your help!
On Fri, Oct 18, 2013 at 5:38 PM, Ben Webb ben@salilab.org wrote:
> On 10/18/2013 02:28 PM, Amjad Farooq wrote: > >> ImportError: No module named modpipe.version >> > > This file should also be generated by Setup, so it suggests that Setup > didn't run properly. Does $MODPIPE/lib/python/modpipe/**version.py exist? > > Ben > -- > ben@salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > ______________________________**_________________ > ModPipe-users mailing list > ModPipe-users@salilab.org > https://salilab.org/mailman/**listinfo/modpipe-usershttps://salilab.org/mailman/listinfo/modpipe-users >
On 10/18/13 2:58 PM, Amjad Farooq wrote: > Yes, ./lib/python/modpipe/version.py exists:
OK then, that means that for some reason your Python path is not being set properly. How *exactly* are you running the demo? If you look at main/AddSeqMP.py, you should see that it adds that lib/python subdirectory to the Python path. So either you're running a different AddSeqMP.py script, or it's not adding the path correctly for some reason.
> But, may be this would help: When I run a test, I get these errors: ... > MissingBinaryError: ModPipe was not configured with CE
This one is surely self explanatory.
> "/alpha/share/software/bioinf/MODPIPE/modpipe220/tests/unit/test_make_chains.py", > line 52, in test_make_one_file > self.assert_(filecmp.cmp(out, '../db/test-pdb.pir')) > AssertionError: False is not True
You'd have to look at the file it produces (out I think is pdb-list.pir) and see what the difference is.
Ben
Thanks Ben!
I got distracted by a couple of other things but I will look into that.
Amjad
On Mon, Oct 21, 2013 at 1:56 PM, Ben Webb ben@salilab.org wrote:
> On 10/18/13 2:58 PM, Amjad Farooq wrote: > >> Yes, ./lib/python/modpipe/version.**py exists: >> > > OK then, that means that for some reason your Python path is not being set > properly. How *exactly* are you running the demo? If you look at > main/AddSeqMP.py, you should see that it adds that lib/python subdirectory > to the Python path. So either you're running a different AddSeqMP.py > script, or it's not adding the path correctly for some reason. > > But, may be this would help: When I run a test, I get these errors: >> > ... > >> MissingBinaryError: ModPipe was not configured with CE >> > > This one is surely self explanatory. > > "/alpha/share/software/bioinf/**MODPIPE/modpipe220/tests/unit/** >> test_make_chains.py", >> line 52, in test_make_one_file >> self.assert_(filecmp.cmp(out, '../db/test-pdb.pir')) >> AssertionError: False is not True >> > > You'd have to look at the file it produces (out I think is pdb-list.pir) > and see what the difference is. > > Ben > -- > ben@salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > ______________________________**_________________ > ModPipe-users mailing list > ModPipe-users@salilab.org > https://salilab.org/mailman/**listinfo/modpipe-usershttps://salilab.org/mailman/listinfo/modpipe-users >
participants (3)
-
Amjad Farooq -
Ben Webb -
Modeller Caretaker