New version of BEDTools includes htslib

verdurin commented 5 years ago

Note that the new version of BEDTools includes htslib. My first quick test build failed, so some changes will be required:

https://github.com/arq5x/bedtools2/releases/tag/v2.28.0

ghuls commented 5 years ago

@verdurin This pull request https://github.com/easybuilders/easybuild-easyconfigs/pull/7962 works for me.

One thing I noticed is that I think BEDtools is never compiled with -march=native

boegel commented 5 years ago

@verdurin Can you elaborate on the problems you ran into?

Other than the changes in sanity_check_paths, the easyconfig contributed by @ghuls in #7962 looks like a pretty straightforward update (unless I'm missing something)...

verdurin commented 5 years ago

I was trying with foss-2018b and first quick attempt saw lots of errors like this:

  * compiling chromsweep.cpp
In file included from bedFile.cpp:12:0:
bedFile.h: In member function ‘void BedFile::reportBedTab(const T&)’:
bedFile.h:47:21: error: expected ‘)’ before ‘PRId64’
 #define PRId_CHRPOS PRId64
                     ^
bedFile.h:942:33: note: in expansion of macro ‘PRId_CHRPOS’
                 printf ("%s\t%" PRId_CHRPOS "\t%" PRId_CHRPOS "\t", bed.chrom.c_str(), start, end);
                                 ^~~~~~~~~~~
bedFile.h:47:21: error: expected ‘)’ before ‘PRId64’
 #define PRId_CHRPOS PRId64
                     ^
bedFile.h:945:33: note: in expansion of macro ‘PRId_CHRPOS’
                 printf ("%s\t%" PRId_CHRPOS "\t%" PRId_CHRPOS "\t%s\t",
                                 ^~~~~~~~~~~
bedFile.h:47:21: error: expected ‘)’ before ‘PRId64’
 #define PRId_CHRPOS PRId64
                     ^
bedFile.h:949:33: note: in expansion of macro ‘PRId_CHRPOS’
                 printf ("%s\t%" PRId_CHRPOS "\t%" PRId_CHRPOS "\t%s\t%s\t",
                                 ^~~~~~~~~~~

It may be that there's no problem with htslib, it's just that the announcement made it sound as though there was more bundling.

ghuls commented 5 years ago

@verdurin I see the same error with foss/2014a tool chain on our old cluster (CentOS6), but no problem with foss/2018a on the new one (CentOS7). BEDtools 2.28.0 switched all integers to int64.

ghuls commented 5 years ago

@verdurin Does this fix it for you?

https://github.com/arq5x/bedtools2/pull/713/commits/9b73bb887db61b256efeec5c44378c46da320e3c

ghuls commented 5 years ago

@verdurin is your glibc version older than 2.18?

boegel commented 4 years ago

@verdurin Can we revisit this?

verdurin commented 4 years ago

@boegel did you want to continue investigating this older version, or just try with a more recent one?

easybuilders / easybuild-easyconfigs

New version of BEDTools includes htslib #7951