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2.0 2.0 3.0 1.72 MB

Integrative Pipeline for Splicing Analyses (IPSA)

License: GNU General Public License v2.0

Perl 65.83% R 3.65% TeX 28.82% Makefile 1.70%

ipsa-full's Issues

Problem installing under Ubuntu

I tried to install the program in Ubuntu and Mac OS X. It has no problems installing in Mac OS X but under Ubuntu the installation stops with the following error:

make[1]: Entering directory `/genedata/Resources/Software/ipsa-full/sjcount-full-3.1'
g++ -I samtools-0.1.18/ j_count.c progressbar.o samtools-0.1.18/libbam.a -lz -o j_count
j_count.c: In function ‘int main(int, char**)’:
j_count.c:255:80: error: conditional expression between distinct pointer types ‘gzFile’ and ‘FILE* {aka _IO_FILE*}’ lacks a cast
         ssj_file = zipped ? gzopen(ssj_file_name,"w") : fopen(ssj_file_name,"w");
                                                                                ^
make[1]: *** [j_count] Error 1
make[1]: Leaving directory `/genedata/Resources/Software/ipsa-full/sjcount-full-3.1'
make: *** [sjcount-full-3.1/sjcount] Error 2

Installation issue: Can't locate Perl/utils.pm in @INC

Hello, I'm trying to install the package. Here is what I did: http://nbviewer.ipython.org/gist/olgabot/1f48a7e73966394464c7

I ran into an error with Perl, and I'm a Perl newbie so this error is hard for me to interpret.

perl Perl/make.pl -repository example/input/ -dir example/output/ -group idrGroup -param '-read1 0' -annot example/hg19v18.gff -genome example/hg19 -merge pooled < example.dat > example.mk
Can't locate Perl/utils.pm in @INC (@INC contains: /opt/biotools/miRDeep2/share/perl5 /opt/biotools/ViennaRNA/lib64/perl5 /projects/ps-yeolab/software/ActivePerl-5.16/site/lib /projects/ps-yeolab/software/ActivePerl-5.16/lib .) at Perl/make.pl line 2.
BEGIN failed--compilation aborted at Perl/make.pl line 2.
make: *** [example.mk] Error 2

After searching around, it seems like the utils.pm file should have come with this module, but Perl can't find it.

Can you help me out? I'm excited to try out this package!
Thanks!
Olga

PS: It would be helpful to have example output figures in the github repo README itself, so someone can see the possibilities of your package without having to install it first.

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