Error while running make

[abolia]

Hi Daniel,

I am trying to install BMFtools after recent changes that were merged today by Brett. While running make, I am getting some errors, not sure what these are. Can you please look into it. Please see below for the error.

Thanks for your help. Ashini

g++ -DBMF_VERSION=\"v1.1-46-g7279\" -std=c++11 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-unused-result -Wno-unused-function -Wuninitialized -Wunreachable-code -pedantic -fno-builtin-gamma -fno-strict-aliasing -fopenmp -Ihtslib -Iinclude -I. -lm -lz -lpthread -finline-functions -O3 -DNDEBUG -flto -fivopts include/sam_opts.o src/bmf_collapse.o include/igamc_cephes.o lib/hashdmp.o src/bmf_rsq.o src/bmf_famstats.o include/bedidx.o src/bmf_err.o lib/kingfisher.o src/bmf_mark.o src/bmf_cap.o lib/mseq.o lib/splitter.o src/bmf_main.o src/bmf_target.o src/bmf_depth.o src/bmf_vet.o src/bmf_sort.o src/bmf_stack.o lib/stack.o src/bmf_filter.o dlib/cstr_util.o dlib/math_util.o dlib/vcf_util.o dlib/io_util.o dlib/bam_util.o dlib/nix_util.o dlib/bed_util.o dlib/misc_util.o libhts.a -lm -lz -lpthread -o bmftools Traceback (most recent call last): File "/uufs/chpc.utah.edu/sys/installdir/xalt/2015-10-13/libexec/xalt_generate_linkdata.py", line 34, in from xalt_transmission_factory import XALT_transmission_factory File "/uufs/chpc.utah.edu/sys/installdir/xalt/2015-10-13/libexec/xalt_transmission_factory.py", line 26, in from XALTdb import XALTdb File "/uufs/chpc.utah.edu/sys/installdir/xalt/2015-10-13/libexec/XALTdb.py", line 99 except ConfigParser.NoOptionError, err: ^ SyntaxError: invalid syntax Traceback (most recent call last): File "/uufs/chpc.utah.edu/sys/installdir/xalt/2015-10-13/libexec/xalt_generate_linkdata.py", line 34, in from xalt_transmission_factory import XALT_transmission_factory File "/uufs/chpc.utah.edu/sys/installdir/xalt/2015-10-13/libexec/xalt_transmission_factory.py", line 26, in from XALTdb import XALTdb File "/uufs/chpc.utah.edu/sys/installdir/xalt/2015-10-13/libexec/XALTdb.py", line 99 except ConfigParser.NoOptionError, err: ^ SyntaxError: invalid syntax

[abolia]

Hey Daniel,

I figured out the issue. Its python version. For these libraries I need python 2.7. Sorry to trouble you. I am closing the issue.

Thanks, Ashini

[dnbaker]

Correct. It's just a problem with your cluster's job management (xalt needs Python 2). I've run into it many, many times. The code still compiles as expected.

Thanks!