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genome / pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

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pindel install fail

wang-xilu opened this issue · comments

commented

The fail result:
Makefile:47: recipe for target 'pindel.o' failed
make[1]: *** [pindel.o] Error 1
make[1]: Leaving directory '/home/amplicon/WXL/pindel/pindel/src'
Makefile:12: recipe for target 'pindel' failed
make: *** [pindel] Error 2

mv: cannot stat 'src/pindel': No such file or directory
mv: cannot stat 'src/pindel2vcf': No such file or directory
mv: cannot stat 'src/sam2pindel': No such file or directory
mv: cannot stat 'src/pindel2vcf4tcga': No such file or directory

Pindel successfully compiled. The pindel executable can be found in this directory.

You can test pindel with the example files in the demo directory; example commands are given in the RUNME in that directory.

For help and background information, see the pindel wiki and its FAQ on gmt.genome.wustl.edu/packages/pindel, as well as
the FAQ file in the Pindel root directory (the same directory as this INSTALL script is located)
or contact us on kaiye@xjtu.edu.cn

commented

I have exactly the same issue:
I ran:
./INSTALL ../htslib/
and i got the following error:

path is now: /home/fabfab/softwares/htslib/
make -C src pindel
make[1] : on entre dans le répertoire « /home/fabfab/softwares/pindel/src »
g++ -I/home/fabfab/softwares/htslib -Wall -g -c -O3 -fopenmp pindel.cpp -o pindel.o
In file included from /home/fabfab/softwares/htslib/htslib/khash.h:131:0,
from pindel.h:34,
from pindel.cpp:35:
/home/fabfab/softwares/htslib/htslib/kstring.h: In function ‘int kputuw(unsigned int, kstring_t*)’:
/home/fabfab/softwares/htslib/htslib/kstring.h:221:9: error: initializer-string for array of chars is too long [-fpermissive]
"90919293949596979899";
^
Makefile:47 : la recette pour la cible « pindel.o » a échouée
make[1]: *** [pindel.o] Erreur 1
make[1] : on quitte le répertoire « /home/fabfab/softwares/pindel/src »
Makefile:12 : la recette pour la cible « pindel » a échouée
make: *** [pindel] Erreur 2

mv: impossible d'évaluer 'src/pindel': Aucun fichier ou dossier de ce type
mv: impossible d'évaluer 'src/pindel2vcf': Aucun fichier ou dossier de ce type
mv: impossible d'évaluer 'src/sam2pindel': Aucun fichier ou dossier de ce type
mv: impossible d'évaluer 'src/pindel2vcf4tcga': Aucun fichier ou dossier de ce type

Pindel successfully compiled. The pindel executable can be found in this directory.

You can test pindel with the example files in the demo directory; example commands are given in the RUNME in that directory.

For help and background information, see the pindel wiki and its FAQ on gmt.genome.wustl.edu/packages/pindel, as well as
the FAQ file in the Pindel root directory (the same directory as this INSTALL script is located)
or contact us on kaiye@xjtu.edu.cn

any idea ?

commented

Ok I got it.
The same issue was posted here:https://github.com/samtools/htslib/issues/771 by @cwrussell and I followed the solutions given by @daviesrob here: https://github.com/daviesrob/htslib/commit/fbbaf9d8b9a1df9243626ead691c2a7f24d6a81a.
I copied/pasted the two new files htslib/kstring.h and htslib/vcf.h from this repo to my computer and ran again the pindel install (./INSTALL ../htslib/), which compiled swiftly this time !

thanks @daviesrob for this fix !

commented

@fabfabBesnard I'm having the same issue but don't see anything when I click on the two links posted above

commented

Dear all,
I think the htslib version may be the reason of install problems.
We have forked pindel to https://github.com/xjtu-omics/pindel and maintain it at xjtu-omics. Please try to clone pindel from https://github.com/xjtu-omics/pindel and then try to install it.

Best
Xiaofei

commented

Hi Claudia,
it's true that my links are no longer working !
Have you tried to copy paste the files from @daviesrob repo (https://github.com/daviesrob/htslib/tree/develop/htslib)to your computer: kstring.h and vcf.h. These files have been changed two months ago, but maybe they will also fix the issue (although they have been changed since the time I used it). I can also transfer you the files I used ?

commented

It isn't a good idea to link to branches in my copy of htslib, as any branch there is liable to be deleted without notice.

The problem you had was fixed in the main htslib repository by this commit, so pindel should work against the current develop branch of HTSlib, at least in this respect.

You may however want to check that no other changes in HTSlib since then are going to cause you problems. See in particular README.large_positions.md which contains important information about recent changes. I've just tried building pindel against this version and it seems to be OK, but it would be good to check in case any incompatibilities have appeared.