lumpy installation in Centos7

[nitha26]

Hi,

I am trying to lumpy in centos7 machine. after downloading the package by git clone
i get following error:

[root@localhost NEW_program]# git clone --recursive https://github.com/arq5x/lumpy-sv.git Cloning into 'lumpy-sv'... remote: Enumerating objects: 3102, done. remote: Total 3102 (delta 0), reused 0 (delta 0), pack-reused 3102 Receiving objects: 100% (3102/3102), 183.53 MiB | 18.57 MiB/s, done. Resolving deltas: 100% (1657/1657), done. Submodule 'lib/htslib' (https://github.com/samtools/htslib.git) registered for path 'lib/htslib' Submodule 'scripts/bamkit' (https://github.com/cc2qe/bamkit.git) registered for path 'scripts/bamkit' fatal: 'validate-git-dir' is not a valid submodule--helper subcommand refusing to create/use '/data1/anupriya_work/Data/NEW_program/lumpy-sv/.git/modules/lib/htslib' in another submodule's git dir

Then i did:

1. cd lumpy-sv
2. make

but I am getting following error: [root@localhost lumpy-sv-0.3.0]# make
autoreconf: 'configure.ac' or 'configure.in' is required cd lib/htslib &&
./configure --disable-bz2 --disable-lzma --enable-libcurl /bin/bash: line 1: ./configure: No such file or directory make: *** [htslib] Error 1

when i checked cd lib/htslib and ls there is no files inside this.
please could you guide me how to install lumpy in centos7.

Thanks you. Nitha

[nitha26]

The above issue is fixed by downloading separately htslib and moving to liband running make command.

[lwtan90]

Thanks! Appreciate if this instruction could be reflected in the installation section.