installation problems

[jjenny]

Hi,

I have htslib installed at ~/bin/htslib-1.11 and demuxlet downloaded to ~/bin/demuxlet.

I also have libtool installed ~/bin/libtool-2.4.6.

When I run autoreconf -vfi, I get:
autoreconf: Entering directory .' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force -I m4 ${ACLOCAL_FLAGS} aclocal: warning: couldn't open directory 'm4': No such file or directory autoreconf: configure.ac: tracing autoreconf: configure.ac: not using Libtool autoreconf: running: /usr/bin/autoconf --force autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing autoreconf: Leaving directory .'

And when I run ./configure --prefix ~/bin/demuxlet/, I get the following error (full config.log attached):

./configure: line 5186: syntax error near unexpected token 2.2' ./configure: line 5186: LT_PREREQ(2.2)'

Any ideas?

Jenny
config.log

[yimmieg]

I think a number of people are having issues with dependencies for demuxlet. Ray, can you work with Anton to fix this? J Sent from a phone. Excuse the typos.

…

On Dec 9, 2020, at 1:57 PM, Jenny Chen ***@***.***> wrote:  Hi, I have htslib installed at ~/bin/htslib-1.11 and demuxlet downloaded to ~/bin/demuxlet. I also have libtool installed ~/bin/libtool-2.4.6. When I run autoreconf -vfi, I get: autoreconf: Entering directory .' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force -I m4 ${ACLOCAL_FLAGS} aclocal: warning: couldn't open directory 'm4': No such file or directory autoreconf: configure.ac: tracing autoreconf: configure.ac: not using Libtool autoreconf: running: /usr/bin/autoconf --force autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing autoreconf: Leaving directory .' And when I run ./configure --prefix ~/bin/demuxlet/, I get the following error (full config.log attached): ./configure: line 5186: syntax error near unexpected token 2.2' ./configure: line 5186: LT_PREREQ(2.2)' Any ideas? Jenny config.log — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[Gvaihir]

htslib 1.11 is not supported, use 1.10.*
#78 (comment)

[jjenny]

Thanks for the quick response - I have switched to htslib 1.10.2 but get the same error messages when trying to compile. What version of gcc do you recommend for compiling?

config.log

[Gvaihir]

Can you use another repo instead: https://github.com/statgen/popscle?

[jjenny]

with popscle I am able to cmake: cmake ../ -DHTS_INCLUDE_DIRS=~/bin/htslib-1.10.2/ -DHTS_LIBRARIES=~/bin/htslib-1.10.2/libhts.a but when I run make I run into this error: [ 2%] Building CXX object CMakeFiles/popscle.dir/allele.cpp.o [ 5%] Building CXX object CMakeFiles/popscle.dir/bam_ordered_reader.cpp.o /n/eddyfs01/home/jjenny/bin/popscle/bam_ordered_reader.cpp: In member function 'void BAMOrderedReader::close()': /n/eddyfs01/home/jjenny/bin/popscle/bam_ordered_reader.cpp:204:11: error: 'nullptr' was not declared in this scope hdr = nullptr; ^ make[2]: *** [CMakeFiles/popscle.dir/bam_ordered_reader.cpp.o] Error 1 make[1]: *** [CMakeFiles/popscle.dir/all] Error 2 make: *** [all] Error 2

…

On Wed, Dec 9, 2020 at 6:10 PM Gvaihir ***@***.***> wrote: Can you use another repo instead: https://github.com/statgen/popscle? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#79 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABHEVDAROJAEFXN3D24GVOLST77WVANCNFSM4UT5IQYQ> .

[hyunminkang]

I pushed a change that solves the compatibility issue with latest htslib (1.11). Let me know if the problem persists.

[Puriney]

I found popscle's docker container makes life smooth. https://github.com/statgen/popscle

[skchronicles]

Solution

For anyone else running into this issue, I found that installing libtool fixes the problem.

Here is a basic sent of instructions that you can follow to install htslib and demuxlet:

# Step 1. Install and build HTSlib 1.10 (required by demuxlet)
# Needs to be a sibling directory to demuxlet install,
# the name of the htslib directory must be called htslib
wget https://github.com/samtools/htslib/releases/download/1.10/htslib-1.10.tar.bz2 \
    && tar -vxjf htslib-1.10.tar.bz2 \
    && rm htslib-1.10.tar.bz2 \
    && cd htslib-1.10 \
    && autoreconf -i \
    && ./configure \
    && make \
    && make install \
    && ln -s /opt2/htslib-1.10 /opt2/htslib \
    && cd ..
 
# Step 2. Install and build demuxlet, the ./configure command 
# needs libtool installed first   
DEBIAN_FRONTEND=noninteractive apt-get install -y libtool \
    && git clone https://github.com/statgen/demuxlet.git \
    && cd demuxlet \
    && autoreconf -vfi \
    && ./configure \
    && make \
    && make install

I hope this helps!

Best Regards,
@skchronicles