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davidroberson / MapSplice2

http://www.netlab.uky.edu/p/bioinfo/MapSplice2
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Make file error in Mapsplice2 #2

Open archu87 opened 6 years ago

archu87 commented 6 years ago

Hi, I am trying to run mapsplice2 but getting error like this

Makefile:189: recipe for target 'bowtie-build' failed make[1]: [bowtie-build] Error 1 make[1]: Leaving directory '/mnt/c/Users/ark446/share/MapSplice2-master/src/MapSplice' Makefile:84: recipe for target 'mapsplice_multi_thread' failed make: [mapsplice_multi_thread] Error 2

Could you please help me on this. Any help is much appreciated.

Thanks

ulah commented 6 years ago

This seems to be a g++ version issue. I get the same error with v5.3, but everything compiles fine with v4.6. Just install that version and change the initial variable declaration in "src/bowtie/Makefile" and "src/MapSplice/Makefile" to point to the v4.6 version. btw: depending on your distro you may afterwards run into a samtools build error (something about lcurses). To resolve that one you simply change lcurses to lncurses at the beginning of the "samtools/Makefile"

sajjanivri commented 5 years ago

Dear Ulah, I have similar problem in my mac os while installing mapSplice2 I am not able to follow your solution, should i install gcc version 4.6 further how and where to change in the makefile you mentioned your help will be highly appreciable

cmonger commented 5 years ago

Also getting this error.

Perhaps the software could be updated to use a system version of bowtie and samtools rather than bundling its own?

chaochaowong commented 4 years ago

I've run into the same errors. It is kind strange for me to get back to gcc version 4.6, since gcc has advanced to v7 already. The version of bowtie and samtools that MapSplice2 intends to build is outdated. Agree with @cmonger that the software should be updated and excluded building bowtie and samtools.