AndreasHeger
commented
6 years ago Thanks, I have trouble reproducing this in a python2.7 environment with a fresh clone.
Open crikkia opened 6 years ago
AndreasHeger
commented
6 years ago Thanks, I have trouble reproducing this in a python2.7 environment with a fresh clone.
Hi,
I have to install pysam from the repository on my user directory because I have no access to the root. I used the command python2.7 setup.py install --user --prefix= but I got the following error message. What is going on? Can I fix something? Thanks in advance
pysam: cython is available - using cythonize if necessary
pysam: htslib mode is shared
pysam: HTSLIB_CONFIGURE_OPTIONS=None
/bin/sh: ./configure: Permission denied /bin/sh: ./configure: Permission denied
pysam: htslib configure options: None
make: execvp: ./version.sh: Permission denied make: execvp: ./version.sh: Permission denied
pysam: htslib_config LIBS=-lz -lm -lbz2 -llzma
pysam: htslib_config PLATFORM=Linux
pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx .o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf _reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram _decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
pysam: htslib_config LDFLAGS=
pysam: config_option: ENABLE_PLUGINS=0
pysam: config_option: HAVE_COMMONCRYPTO=0
pysam: config_option: HAVE_GMTIME_R=0
pysam: config_option: HAVE_HMAC=0
pysam: config_option: HAVE_IRODS=0
pysam: config_option: HAVE_LIBCURL=0
pysam: config_option: HAVE_MMAP=0
running install running bdist_egg running egg_info writing pysam.egg-info/PKG-INFO writing top-level names to pysam.egg-info/top_level.txt writing dependency_links to pysam.egg-info/dependency_links.txt package init file 'samtools/init.py' not found (or not a regular file) package init file 'bcftools/init.py' not found (or not a regular file) package init file 'samtools/win32/init.py' not found (or not a regular file) package init file 'htslib/init.py' not found (or not a regular file) package init file 'htslib/htslib/init.py' not found (or not a regular file) reading manifest file 'pysam.egg-info/SOURCES.txt' writing manifest file 'pysam.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py copying pysam/config.py -> build/lib.linux-x86_64-2.7/pysam copying htslib/config.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) building 'pysam.libcbcftools' extension gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-p rotector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE - fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/panfs/panfem/fem0/keu_crava/pysam-master/htslib -I/panfs/panfem/fem0/keu_crava/pysam-master/samtools -I/panfs/panfem/fem0/keu_crava/pysam-master/bcftools -I/panfs/panfem/fem0/keu_crava/pysam-master/pysam -/panfs/panfem/fem0/keu_crava/pysam-master -I/usr/include/python2.7 -c pysam/libcbcftools.c -o build/temp.linux-x86_64-2.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -W no-sign-compare -Wno-error=declaration-after-statement pysam/libcbcftools.c:523:28: fatal error: bcftools.pysam.h: No such file or directory
include "bcftools.pysam.h"
compilation terminated. error: command 'gcc' failed with exit status 1