MinPath error in HUMAnN2 with OS X

[NORIHO IIDA]

Hi all,

I have recently installed humann2, but I got an error while trying the demo. The error is as follows:

Computing pathways abundance and coverage ...
Traceback (most recent call last):
  File "/macqiime/lib/python2.7/site-packages/humann2-0.1.9-py2.7.egg/humann2/quantify/MinPath12hmp.py", line 26, in <module>
    for file in os.listdir(minpath):
OSError: [Errno 2] No such file or directory: '/macqiime/lib/python2.7/site-packages/humann2-0.1.9-py2.7.egg/humann2/quantify/MinPath'
Traceback (most recent call last):
  File "/macqiime/lib/python2.7/site-packages/humann2-0.1.9-py2.7.egg/humann2/quantify/MinPath12hmp.py", line 26, in <module>
    for file in os.listdir(minpath):
OSError: [Errno 2] No such file or directory: '/macqiime/lib/python2.7/site-packages/humann2-0.1.9-py2.7.egg/humann2/quantify/MinPath'

It seems that MinPath didn't work properly in my OS X with HUMAnN2.

I did $ python setup.py minpath --update-glpk to install MinPath, but several warning appeared after the command was executed.

1 warning generated.
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I. -I./amd -I./bflib -I./cglib -I./colamd -I./env -I./minisat -I./misc -I./proxy -I./zlib -g -O2 -MT libglpk_la-wclique.lo -MD -MP -MF .deps/libglpk_la-wclique.Tpo -c misc/wclique.c -o libglpk_la-wclique.o >/dev/null 2>&1
mv -f .deps/libglpk_la-wclique.Tpo .deps/libglpk_la-wclique.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..  -I. -I./amd -I./bflib -I./cglib -I./colamd -I./env -I./minisat -I./misc -I./proxy -I./zlib   -g -O2 -MT libglpk_la-wclique1.lo -MD -MP -MF .deps/libglpk_la-wclique1.Tpo -c -o libglpk_la-wclique1.lo `test -f 'misc/wclique1.c' || echo './'`misc/wclique1.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I. -I./amd -I./bflib -I./cglib -I./colamd -I./env -I./minisat -I./misc -I./proxy -I./zlib -g -O2 -MT libglpk_la-wclique1.lo -MD -MP -MF .deps/libglpk_la-wclique1.Tpo -c misc/wclique1.c  -fno-common -DPIC -o .libs/libglpk_la-wclique1.o
In file included from misc/wclique1.c:24:
./env/env.h:32:9: warning: 'SIZE_T_MAX' macro redefined
#define SIZE_T_MAX (~(size_t)0)
        ^
/usr/include/i386/limits.h:98:9: note: previous definition is here
#define SIZE_T_MAX      ULONG_MAX       /* max value for a size_t */
        ^
1 warning generated.

Please could you give me advice for this probelm.

I appreciate you in advance,

Noriho

[Lauren McIver]

Hi Noriho,

I agree with you that it looks like minpath did not install properly. I think the warning messages from installing glpk might be okay. It looks like the issue is that minpath is not included in the humann2 install. My suggestion would be to rerun the humann2 install command (ie "python setup.py install") and then try the demo again. Please let me know if this fixes the issue.

Thank you,

Lauren

[NORIHO IIDA]

Hi Lauren,

Thank you for the reply. After re-install humann2, minpath worked!
Thank you,

Noriho

[Ming Liao]

Hello, all

I got the same problem. But since I was not allowed to use the linux server to connect any websites. As the "python install setup.py" required the internet access, it is not surprised to see that my minpath can not be installed.

The humann2 installation tutorial did not provide any commands to by pass the minpath installation. I am wondering can I download the minpath, then change the $PATH so that humann2 can use it?

Thanks


Ming

[Ming Liao]

By the way, I have tried to add the MinPath to the PATH, but it failed.....

Can anyone show me some alternative way s(instead of installing through python install setup.py) to install MinPath so that humann2 can use it? Thanks.

Best,

Ming

[Ming Liao]

Hello, all

I think I have made it. Thanks to Yunli's question here:
https://groups.google.com/forum/#!topic/humann-users/MSVmXC7DSW0

After I follow Lauren's instruction to have glpk installed correctly, the humann2 can run with MinPath. I checked the humann2/quantify directory, there was one file named "MinPath12hmp.py".

One question: The original file in MinPath installation directory was "MinPath1.2.py". If I replaced the "MinPath12hmp.py" with this "MinPath1.2.py", can humann2 still work?

Or I renamed this "MinPath1.2.py" into "MinPath12hmp.py", then copied it to the humann2/quantify directory and replaced the original one, can humann2 still work?


I am just curious about this. Thanks

Ming