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: "pindel.h:34:26: fatal error: htslib/khash.h: No such file or directory
I read a post the same issue, and I followed what they say:
-Install XCode command line tools (run "
-I downloaded and compiled samtools 0.1.18
But it is still failing.
Maybe on issue is that I have several samtools version installed:
samtools-0.1.18 + samtools-0.1.19 + samtools-1.2 in my computer
I read that pindel only works with 0.1.18, that's why I installed it also. I have several khash.h files in my system, but it seems that pindel does not find them:
find $HOME -name khash.h
find: /Users/lab/Public/.TemporaryItems/folders.502: Permission denied
I tried to run pindel by specifying all different samtools folder: nothing works. Exple
./INSTALL /mypathto/samtools-0.1.18/" or ./INSTALL /mypathto/samtools-0.1.19/" or ./INSTALL /mypathto/samtools-1.2/" or "./INSTALL /mypathto/samtools-1.2/htslib-1.2.1/
I also tried to make a new htslib dir in samtools-0.1.18 folder + copy khash.h file into it and run pindel with "./INSTALL /mypathto/samtools-0.1.18/" but it still does not work.
I am lost and downhearted now... Any tips ?