Pb to Compile Pindel on MacOs x

Question

[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:

pindel.h:34:26: fatal error: htslib/khash.h: No such file or directory
compilation terminated.

I read a post the same issue, and I followed what they say:

• Install MacPorts (and I had to self-update via the tarball, as explained here) and gcc (gcc47)
• Install XCode command line tools (run xcode-select --install)
• Download and compile 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
/Users/lab/TOOLS_VariantAnalysis/bwa-0.7.8/khash.h
/Users/lab/TOOLS_VariantAnalysis/htslib-1.2.1/htslib/khash.h
/Users/lab/TOOLS_VariantAnalysis/htslib-master/htslib/khash.h
/Users/lab/TOOLS_VariantAnalysis/samtools-0.1.18/khash.h
/Users/lab/TOOLS_VariantAnalysis/samtools-0.1.19/khash.h
/Users/lab/TOOLS_VariantAnalysis/samtools-1.2/htslib-1.2.1/htslib/khash.h

I tried to run pindel by specifying all different samtools folder: nothing works. Example

./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?

Fabrice

Answer 1

[fbesnard]

Hi,

I had to pause this, but I just went back to it after three months. Finally it worked. I did as suggested by John:

./INSTALL /mypathto/samtools-1.2/htslib-1.2.1

The reason why it was not working is that I realized I had to delete the pindel folder after each failed compilation. When I started to install it form a fresh git-cloned folder, this times it worked.

[lanhaitun1987]

That's completely right. First delete the pindel folder, then unzip pindel.zip and cd pindel ./INSTALL /PATH/htslib-x.x.x .

Answer 2

[John Marshall]

The message

pindel.h:34:26: fatal error: htslib/khash.h​

indicates that you are using the current master branch from the git repository, which has been converted to build with htslib rather than the legacy samtools API. Hence, as the instructions in INSTALL note, you should succeed with the htslib subdirectory of 1.x samtools or an htslib:

./INSTALL /mypathto/samtools-1.2/htslib-1.2.1
./INSTALL /mypathto/htslib-1.2.1

but it will not work with samtools 0.1.19 or any other samtools 0.1.x.

What errors were produced when you ran ./INSTALL with the htslib-1.2.1 directory (which you need to have already built by typing make in its directory)?

Note that you will also need to be building Pindel with an OpenMP-capable compiler, which is somewhat non-trivial on OS X.

[fbesnard]

Hi John,

Thank you for your help.

As you recommended, I ran make in htslib-1.2.1 folder of samtools-1.2. Then in the pindel folder, I ran ./INSTALL /Users/lab/TOOLS_VariantAnalysis/samtools-1.2/htslib-1.2.1/, and I get again the same error list of error messages during the compilation, all ending by:

pindel.h:34:26: fatal error: htslib/khash.h: No such file or directory
compilation terminated.

By the way, what is a OpenMP-capable compiler? Is gcc47 not sufficient?

[John Marshall]

Are you sure you have not mistyped /Users/lab/TOOLS_VariantAnalysis/samtools-1.2/htslib-1.2.1/?

[fbesnard]

Quite sure, yes, I got it by automatic completion with the tab key.