Installation error of hmmer
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0
Entering edit mode
5 months ago

I have installed this software and then tried to remove it with the command (sudo apt-get remove hmmer) but it does not work. It created some binary files in usr/local/bin

(base) omic@omics-world-001:~/Downloads/hmmer-2.3.2$ make check
(cd testsuite; make check)
make[1]: Entering directory '/home/omic/Downloads/hmmer-2.3.2/testsuite'

Running test suite exercises.
Warning: some tests may take several minutes to complete.

./sqc 2 exercises.sqc . ../src
Can't locate getopts.pl in @INC (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at ./sqc line 179.
make[1]: *** [Makefile:59: check] Error 2
make[1]: Leaving directory '/home/omic/Downloads/hmmer-2.3.2/testsuite'
make: *** [Makefile:99: check] Error 2
(base) omic@omics-world-001:~/Downloads/hmmer-2.3.2$ make install
mkdir -p /usr/local/bin
mkdir -p /usr/local/man/man1
for file in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch ; do\
   cp src/$file /usr/local/bin/;\
done
cp: cannot create regular file '/usr/local/bin/hmmalign': Permission denied
cp: cannot create regular file '/usr/local/bin/hmmbuild': Permission denied
cp: cannot create regular file '/usr/local/bin/hmmcalibrate': Permission denied
cp: cannot create regular file '/usr/local/bin/hmmconvert': Permission denied
cp: cannot create regular file '/usr/local/bin/hmmemit': Permission denied
cp: cannot create regular file '/usr/local/bin/hmmfetch': Permission denied
cp: cannot create regular file '/usr/local/bin/hmmindex': Permission denied
cp: cannot create regular file '/usr/local/bin/hmmpfam': Permission denied
cp: cannot create regular file '/usr/local/bin/hmmsearch': Permission denied
make: *** [Makefile:114: install] Error 1
hmmer Linux bash • 373 views
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Entering edit mode
5 months ago
zorbax ▴ 610

Two issues here, you are required to install a Perl module, using apt in Ubuntu or cpan: sudo apt install libperl4-corelibs-perl or perl -MCPAN -e shell install Perl4::CoreLibs. Second, you require sudo to install in /usr/local: sudo make install. It would be easier to install it using Conda, but I'm not sure whether your version is available there.

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