Question: stampy install error??
1
gravatar for Cherry
4.4 years ago by
Cherry50
Germany
Cherry50 wrote:

Hi, everyone!I am a new one to bioinformatic. So please forgive I am so clumsy. I have an issue when installing stampy to cluster and I am not sure how to fix it.

I download stampy-1.0.23 (I think it is the newest one), run "make" and then it said:

make[1]: Entering directory `/home/**/programs/stampy-1.0.23'
make[2]: Entering directory `/home/**/programs/stampy-1.0.23'
cp -r build/python2.7/* .
g++ `python2.7-config --ldflags` -pthread -shared -Wl build/linux-x86_64-2.7-ucs2/pyx/maptools.o build/linux-x86_64-2.7-ucs2/c/maputils.o build/linux-x86_64-2.7-ucs2/c/alignutils.o build/linux-x86_64-2.7-ucs2/readalign.o build/linux-x86_64-2.7-ucs2/algebras.o build/linux-x86_64-2.7-ucs2/frontend.o -o maptools.so
make[2]: Leaving directory `/home/**/programs/stampy-1.0.23'
make[1]: Leaving directory `/home/**/programs/stampy-1.0.23'

Does anybody know what happened and how should I do?

 

software error • 2.8k views
ADD COMMENTlink written 4.4 years ago by Cherry50

Do you have any type of error message printed out on screen?

ADD REPLYlink written 4.4 years ago by iraun3.5k

Hi airan,

Nothing else. That were all the messages I have got.

Did I succeed or fail to install?

ADD REPLYlink written 4.4 years ago by Cherry50

If you don't have any error message I guess that it is OK. You can try to run stampy and see what happens:

./stampy.py --help
ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by iraun3.5k
1

I typed "./stampy.py --help" and I got:

Could not import the maptools module -- does the maptools.so library exist?
Traceback (most recent call last):
  File "./stampy.py", line 14, in <module>
    import maptools
  File "maptools.pyx", line 4, in init maptools (pyx/maptools.c:25713)
  File "/Net/fs1/home/gerton/Progs/Mapper/stampy/Stampy/utils.py", line 3, in <module>
  File "/Net/fs1/home/gerton/Progs/Mapper/stampy/Stampy/genome.py", line 18, in <module>
  File "/Net/fs1/home/gerton/Progs/Mapper/stampy/Stampy/filez.py", line 1, in <module>
  File "/Net/fs1/home/gerton/Progs/Mapper/stampy/Stampy/gzip.py", line 9, in <module>
    import zlib
ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /data/home/di98zud2/local/lib/python2.7/lib-dynload/zlib.so)

 

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by Cherry50

You have errors related to python installation... have you read this?: http://www.well.ox.ac.uk/~gerton/README.txt

In the 2. Building part, you can see the most common problems during stampy installation. Check python installation issues and install again.

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by iraun3.5k

Hi airan, thanks a lot!

Actually, I have read but I failed to fix it.

Anyway, I will try to install python again and then stampy.

Hope it will work!

ADD REPLYlink written 4.4 years ago by Cherry50
1

BTW, to fix the error "ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /data/home/di98zud2/local/lib/python2.7/lib-dynload/zlib.so)", try running this:

sudo apt-get update
sudo apt-get install libc6

 

You need to upgrade your libc6 package because Stampy was compiled against glibc version 2.14, and it requires that version to run, but your system has an older version installed.

ADD REPLYlink written 4.4 years ago by iraun3.5k
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