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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.
GNU General Public License v3.0
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pindel install fail #52

Open sclirl opened 8 years ago

sclirl commented 8 years ago

My install steps are:

  1. install htslib-develop unzip htslib-develop.zip cd /home/sclirl/Tools/htslib-develop ./configure --prefix=/home/sclirl/Tools/htslib-develop make make install (This is ok!)
  2. install pindel cd /home/sclirl/Tools/pindel-master ./INSTALL /home/sclirl/Tools/htslib-develop but fail as follows, any help would be appreciated! Thanks!

The fail result: path is now: /home/sclirl/Tools/htslib-develop/ make: * No rule to make target Makefile.local', needed bypindel'. Stop. If this is the first time you're running this install script please wait a moment as we create the Makefile.local make -C src pindel make[1]: Entering directory /home/sclirl/Tools/pindel-master/src' make[1]: Leaving directory/home/sclirl/Tools/pindel-master/src' make[1]: Entering directory `/home/sclirl/Tools/pindel-master/src' g++ -I/home/sclirl/Tools/htslib-develop/include -Wall -g -c -O3 -fopenmp pindel.cpp -o pindel.o g++ -I/home/sclirl/Tools/htslib-develop/include -Wall -g -c -O3 -fopenmp reader.cpp -o reader.o In file included from reader.cpp:40: refreader.h:6:1: warning: null character(s) ignored reader.cpp: In function 'void GetOneChrSeq(std::ifstream&, std::string&, bool)': reader.cpp:168: error: 'RefReader' was not declared in this scope reader.cpp:168: error: 'rr' was not declared in this scope reader.cpp:168: error: expected type-specifier before 'RefReader' reader.cpp:168: error: expected ';' before 'RefReader' reader.cpp:170: error: type '' argument given to 'delete', expected pointer make[1]: * [reader.o] Error 1 make[1]: Leaving directory`/home/sclirl/Tools/pindel-master/src' make: *\ [pindel] Error 2

INSTALL failed Possible reasons:

  1. 'cannot cd to [path] ->the htslib path provided was incorrect
  2. 'cannot find -lbam' ->htslib was not properly compiled/made, in that case, go to the htslib directory and follow the htslib installation instructions and run 'make'.

For further help, see the FAQ file included in this directory Or contact us on kaiye@xjtu.edu.cn

dpaulino commented 7 years ago

I am having the same issue. Have others found a solution?

EWLameijer commented 7 years ago

This error message ("refreader.h:6:1: warning: null character(s) ignored") implies that the refreader.h file has been corrupted somehow (for example, by opening/editing it with a Windows application or whatever).

My first recommendation would be to clone the latest Pindel version, under OSX or (preferably) Linux/Unix: (git clone https://github.com/genome/pindel) and try install again

If you get the same "null character" warning, I'd open the file on which the problem is reported in an editor and copy-paste its contents to a new file, deleting the old file and giving the new file the name of the old file. Or perhaps by copy-pasting it from Github directly. In any case, this seems to be a file corruption problem of unknown origin.

If none of this seems to work, please let us know!

Krisloveless commented 7 years ago

59 I tried this by adding "/lib" and it worked. @dpaulino @sclirl