Troubles Installing Qpalma To Run Palmapper ...
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11.0 years ago
Geparada ★ 1.5k

Hi!!

I spend the last hours trying to install QPALMA. When I run setup_qpalma.sh it's fails:

   geparada@splicing:~/qpalma-0.9.3$ ./setup_qpalma.sh
Warning: variable QPALMA_PATH not set; consider running ./setup_qpalma.sh
QPalma setup script (version 1.0)
===================================

QPalma base directory (currently set to "", suggest to set to "/home/geparada/qpalma-0.9.3")
/home/geparada/qpalma-0.9.3    #I put exactly the suggested dir
=> Setting QPALMA base directory to "/home/geparada/qpalma-0.9.3"

PALMapper base directory (currently set to "")
/home/geparada/palmapper-0.4-rc3        #I previously installed PALMapper
=> Setting PALMapper base directory to "/home/geparada/palmapper-0.4-rc3"

Which optimizer should be used:
1. Mosek (commercial optimizer with available trial license)
2. CVXOPT (free optimizer)
2

To install CVXOPT, download it from
http://abel.ee.ucla.edu/cvxopt/download/index.html
and follow the instructions.

CVXOPT installation bin directory (currently set to "")
/home/geparada/cvxopt-1.1.3        #I really don't know if it is the bin directory
=> Setting CVXOPT bin directory to "/home/geparada/cvxopt-1.1.3"

Compiling modules:

1. Parameter Parser Module
--------------------------
g++ -Wall -Wshadow -std=c++98 -O3 -fPIC `python-config --cflags`   -c -o ParaParser.o ParaParser.cpp
/bin/sh: python-config: not found
In file included from ParaParser.cpp:1:0:
ParaParser.h:4:20: fatal error: Python.h: No such file or directory
compilation terminated.
make: *** [ParaParser.o] Error 1
geparada@splicing:~/qpalma-0.9.3$

I think there are some kind of trouble with CVXOPT, but apparently it's well installed because I don't get any error when I test it:

$:~/Downloads/cvxopt-1.1.3/examples/doc/chap8$ python lp.py
    pcost       dcost       gap    pres   dres   k/t
 0: -8.1000e+00 -1.8300e+01  4e+00  0e+00  8e-01  1e+00
 1: -8.8055e+00 -9.4357e+00  2e-01  1e-16  4e-02  3e-02
 2: -8.9981e+00 -9.0049e+00  2e-03  3e-16  5e-04  4e-04
 3: -9.0000e+00 -9.0000e+00  2e-05  9e-17  5e-06  4e-06
 4: -9.0000e+00 -9.0000e+00  2e-07  1e-16  5e-08  4e-08
Optimal solution found.

x =

[ 1.00e+00]
[ 1.00e+00]

I really don't know what else to do...

Are there some one that successfully installed QPALMA?

Thanks for your time!

next-gen sequencing mapping installation • 3.0k views
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is there a file named "Python.h" in the path returned by "python-config --cflags" ?

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Using $ locate Python.h, I found one file named Python.h, there is in /usr/include/python2.7_d/Python.h ... but I don't know how to check if is in the "python-config --cflags" ...

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Using $ locate Python.h, I found one file named Python.h, there is in /usr/include/python2.7_d/Python.h ... but I don't know how to check if is in the "python-config --cflags" path ...

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11.0 years ago

The trouble seems to come from:

/bin/sh: python-config: not found

Is python-config in your path? Mine is located under /usr/bin/python-config.

Cheers, Gunnar

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Thanks Gunnar!! I didn't had the python-config file, then installed the python-dev package and now the problem is solved!!

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