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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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htslib compilation error. #77

Open chirrie opened 6 years ago

chirrie commented 6 years ago

I am getting the error below on compiling htslib on using make and make INSTALL on the cluster... but when I use make and sudo make INSTALL on personal PC it works well. Is their a way I can compile htslib without requring the sudo rights? compilation terminated. In file included from search_MEI.cpp:15:0: pindel.h:34:26: fatal error: htslib/khash.h: No such file or directory

include "htslib/khash.h"

                      ^

compilation terminated. In file included from search_MEI_util.h:26:0, from search_MEI_util.cpp:21: pindel.h:34:26: fatal error: htslib/khash.h: No such file or directory

include "htslib/khash.h"

                      ^

compilation terminated. In file included from fn_parameters.cpp:10:0: pindel.h:34:26: fatal error: htslib/khash.h: No such file or directory

include "htslib/khash.h"

                      ^

compilation terminated. In file included from user_defined_settings.cpp:9:0: pindel.h:34:26: fatal error: htslib/khash.h: No such file or directory

include "htslib/khash.h"

                      ^

compilation terminated. In file included from pindel_read_reade

minghao4 commented 6 years ago

Hi, I recently had a similar issue.

I don't know if you still need help or if this solution would work with your exact issue, but for anyone looking at this in the future, what I did was to literally copy the htslib folder (e.g. htslib-1.8/htslib) into pindel/src and it compiled.

fizwit commented 6 years ago

pindel requires include files from both HTSlib and SAMtools. SAMtools and HTSlib version 1.8 has been split into two different installs. Use CPATH to specify the include path to both SAMtools and HTSlib before executing INSTALL.

// HTSLIB_HOME is the path to your HTSLIB install export CPATH=$HTSLIB_HOME/include:$SAMTOOLS_HOME/include

jmarshall commented 6 years ago

@fizwit: Building pindel no longer (since PR #12) requires anything from SAMtools. (There is one remaining minor error in some error message text in the INSTALL script: see PR #18.)