Pindel during compile : pindel.h:35:24: error: htslib/sam.h: No such file or directory

When I tried to compile Pindel using the following command :

./INSTALL /data/tam/script/samtools-1.5/

The following error (partially) appeared :

pindel.h:34:26: error: htslib/khash.h: No such file or directory
pindel.h:35:24: error: htslib/sam.h: No such file or directory
In file included from refreader.cpp:26:
pindel.h:34:26: error: htslib/khash.h: No such file or directory
pindel.h:35:24: error: htslib/sam.h: No such file or directory
In file included from searcher.cpp:22:
pindel.h:34:26: error: htslib/khash.h: No such file or directory
pindel.h:35:24: error: htslib/sam.h: No such file or directory
In file included from reporter.cpp:32:
pindel.h:34:26: error: htslib/khash.h: No such file or directory
pindel.h:35:24: error: htslib/sam.h: No such file or directory
reader.cpp:29:24: error: htslib/sam.h: No such file or directory
reader.cpp:30:28: error: htslib/kstring.h: No such file or directory
reader.cpp:31:25: error: htslib/kseq.h: No such file or directory
reader.cpp:32:26: error: htslib/khash.h: No such file or directory
reader.cpp:33:26: error: htslib/ksort.h: No such file or directory

Is it I have to add a path to the htslib directory? Use what command?

Thank you!

pindel htslib

• 4,734 views • link

updated 8.8 years ago by Biostar

• written 8.9 years ago by johnnytam100

Where and how did you get your samtools? There should be a htslib folder in /data/tam/script/samtools-1.5/. Is it not there?

• 0 views • link

written 8.9 years ago by GenoMax

0 answers

No answers yet.

More posts like this

293 Killed error when running GCTA in WSL
written 3.6 years ago by itsmesmb •

Dear all, I'm running GWAS in GTCA with the parameter shown below. However, I end up having an error, what is the source of this …
Pindel installation failing due to htslib
written 6.7 years ago by cdastmalchi •

I have made the following Dockerfile to install pindel: # Use Python base image from DockerHub FROM python:2.7 RUN apt-get update && apt-get install -y …
working with Sanger fasta + qual + clip files
written 7.4 years ago by sullis02 •

I have an old Sanger fasta file and its associated qual file, as well as a 'clip' file that shows where to trim low-quality sequence …
MGRA returns error
written 7.5 years ago by little_more •

I'm using MGRA server (http://mgra.cblab.org/) to reconstruct rearrangement history but it returns an error. I hope someone here has used this server and knows what …
Can I read chrom, strand, pos, len from bam files without htslib?
written 7.8 years ago by Click downvote

I am having trouble compiling my program when I use htslib. Since this is software many other people are likely to use, I imagine my …
Error downloading MuSiC2
written 8.0 years ago by Gene_MMP8

I am following all the steps that are required to install music2. I am trying to download calcRoiCovg in one of the steps. I have …
Issues installing Pindel from git
written 8.8 years ago by jsneaththompson

I'm currently attempting to install Pindel on my ubuntu machine (16.04 server), but have been having issues with running the ./INSTALL file. The ./INSTALL file …
Build Bowtie2 2.3.3.1 with make on linux 64 bit
written 8.8 years ago by marongiu.luigi

Hello, I am trying to build [bowtie 2 version 2.3.3.1][1] from source using the command make but I get the following: /bowtie2$ make g++ -O3 …
Bowtie2 Build error in CygWin
written 9.3 years ago by NGS-Newbie •

Hi All I am trying to build bowtie2 on cygwin (Windows10). I tried to "make" it from the source file. 1) Even after installing Thread …
Pb to Compile Pindel on MacOs x
written 11.2 years ago by fbesnard •

Hi everyone, I cannot compile Pindel on my MacOSX 10.9.5. In my pindel dir, I ran: `./INSTALL /Users/lab/TOOLS_VariantAnalysis/samtools-0.1.18/` and I get the following message: ``` …