0.44.0 cmake does not run autoreconf for htslib

[ilovezfs]

This results in build failure.

/bin/sh: /tmp/kallisto-20180215-71993-1fpw0fo/kallisto-0.44.0/ext/htslib/configure: No such file or directory
make[3]: *** [ext/htslib/src/htslib-stamp/htslib-configure] Error 127
make[2]: *** [CMakeFiles/htslib.dir/all] Error 2
make[1]: *** [CMakeFiles/htslib.dir/rule] Error 2
make: *** [htslib] Error 2

[mfansler]

Same.

[mr-eyes]

I've solved the htslib error(s) through these steps.

1- Clone the htslib "https://github.com/samtools/htslib" 2- Build it once, then keep this directory 3- Remove the htslib from Kallisto/ext 4- Copy the htslib directory you kept from step 2 to kallisto/ext/ 5- build the kallisto

---

Auto build bash script I wrote for development purpose that I need to build Kallisto many times.

rm -rf -f kallisto/build rm -rf kallisto/ext/htslib cp -r htslib kallisto/ext/ mkdir kallisto/build cd kallisto/build cmake .. make

[mj-harvey]

do an "autoreconf" in the ext/htslib directory (autoconf and automake packages required)

[boryanakis]

I was running into the same problem. @mj-harvey's suggestion worked once I had also installed libtool. Without it, I kept getting this error: configure.ac:26: error: possibly undefined macro: m4_esyscmd_s. Thanks!