cannot find input file htslib/Makefile.in

[davismcc]

Hi Hyun

This looks like a fantastic set of tools. I came across your prepring on demultiplexing "natural barcodes" in single-cell data. This is relevant to some things we're working on, so I'm keen on trying the demuxlet tool.

Unfortunately I'm having trouble installing APIgenome. I get an error from ./configure complaining that it cannot find htslib/Makefile.in:

[...tuncated output...]
checking for pfbtops... yes
checking for gnuplot... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating libnmf/Makefile
config.status: error: cannot find input file: `htslib/Makefile.in'
(py3) [davis@hh-yoda-04-01 apigenome]$ make
CDPATH="${ZSH_VERSION+.}:" && cd . && aclocal-1.14 -I m4
/bin/sh: aclocal-1.14: command not found
make: *** [Makefile:381: aclocal.m4] Error 127

Can you tell what I'm doing wrong there?

Thanks!
Davis

[Griffan]

I think you might need to run:
autoheader && autoconf && htslib/configure

[davismcc]

Thanks for the suggestion. This just gives me the following, though:

[apigenome]$ autoheader && autoconf && htslib/configure
bash: htslib/configure: No such file or directory

There is indeed no "configure" file in the htslib directory, although there is a "config.h" file and a "configure.ac" file. Do I need to install htslib in that directory?

Best
Davis

[Griffan]

I mean you could run this line autoheader && autoconf && configure in htslib/ directory, this should fix the problem, but it might not be the official solution.

[stetner]

I found the following - no Makefile.in in the htslib directory caused

./configure --prefix /my/prefix/

to fail. My solution was to cd to htslib

autoheader && autoconf && configure --prefix /my/prefix/

It does not produce the Makefile.in so I copied the Makefile to Makefile.in and then cd back up into the apigenome directory and ran

./configure --prefix /my/prefix/
make
make install

there and it has all seemed to work.

[hyunminkang]

My apologies for the late response. Although this issue has not been completely resolved due to pending changes, you can visit https://github.com/statgen/demuxlet if you're interested in getting demuxlet.