compilation

[colindaven]

Interesting.

Any ideas why it's not picking up zlib.h despite the package being present?

sudo apt install zlib1g-dev
Reading package lists... Done
Building dependency tree       
Reading state information... Done
zlib1g-dev is already the newest version (1:1.2.8.dfsg-2ubuntu4.1).


(base) rcug@hpc01:/mnt/ngsnfs/tools/CONSENT$ sudo apt install zlib1g-dev
Reading package lists... Done
Building dependency tree       
Reading state information... Done
zlib1g-dev is already the newest version (1:1.2.8.dfsg-2ubuntu4.1).
0 upgraded, 0 newly installed, 0 to remove and 71 not upgraded.
(base) rcug@hpc01:/mnt/ngsnfs/tools/CONSENT$ bash install.sh 
make: Nothing to be done for 'default'.
make: 'poa' is up to date.
make: Nothing to be done for 'all'.
/mnt/ngsnfs/tools/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  bseq.c -o bseq.o
bseq.c:1:10: fatal error: zlib.h: No such file or directory
 #include <zlib.h>
          ^~~~~~~~
compilation terminated.
make: *** [Makefile:29: bseq.o] Error 1

[morispi]

Hey,

This actually seems to be an issue related to minimap2.
From what I see, the install script seems to fail while in that directory.

Could you please confirm by cd-ing into the minimap2 folder and try to run make there?

Pierre

[colindaven]

Hi Pierre,

thanks, you can disregard. It was a mistake on my side forgetting to disable the miniconda3 repo, which I use by default.

conda deactivate 
and 
bash install.sh 
worked perfectly then

Thanks.
Colin