Entering edit mode
3.4 years ago
shpak.max
▴
50
I obtained the most recent version of Stampy from github, and makefile execution fails.
Specifically, as instructed I ran
make python=python2.7
because the default python is 3 on our server, and I get the following error. I'm not sure what to do about the fatal error: Python.h No file or directory and the python2.7-config command not found. I have a standard installation of Python 2.7.18
sudo make python=python2.7
make[1]: Entering directory '$HOME/alignment_software/stampy'
mkdir -p build//pyx
ln -s -f `pwd`/pyx/ucs4/maptools.c pyx/maptools.c
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `python2.7-config --includes` -c pyx/maptools.c -o build//pyx/maptools.o
/bin/bash: python2.7-config: command not found
pyx/maptools.c:4:10: fatal error: Python.h: No such file or directory
4 | #include "Python.h"
| ^~~~~~~~~~
compilation terminated.
make[1]: *** [makefile:39: build//pyx/maptools.o] Error 1
Can I ask why specifically stampy? I myself date back from the time that aligner was cutting-edge (so I liked that one as well), however recent aligners are much more performant and accurate.
I inherited a pipeline for an unfinished data analysis project and wanted my results to be consistent with those of my predecessor on the study.
What newer tools accomplish the same things as stampy (i.e. optimized for alignments of CNV-rich regions and other reads that BWA etc may miss)?
valid reason indeed :)
it seems indeed you ran into some technical issue there, perhaps still a conflict in the python versions? I'm no expert in this so can't help you much further I'm afraid.
What are your preferred, more up to date aligners? If I can't get stampy to work, I may need to use something else to pick up on the CNV-enriched reads that BWA couldn't align, even if it means some inconsistency with the analyses that my predecessor performed.