traviswheelerlab / mirage Goto Github PK

Mirage generates multiple sequence alignments of proteoforms by mapping sequences back to their coding regions on the genome and then compressing those mappings into alignments.

License: BSD 3-Clause "New" or "Revised" License

Perl 73.13% C 24.69% Shell 1.87% CMake 0.31%

bioinformatics biology proteoforms

mirage's People

Contributors

Stargazers

Watchers

Forkers

penny1533 rsuchecki nasa03 rnaimehaom

mirage's Issues

build failed on m1 Mac

  [mirage2 dependencies test  1/27]: blat test 1...make[2]: *** [CMakeFiles/build-dependencies] Error 1
make[1]: *** [CMakeFiles/build-dependencies.dir/all] Error 2
make: *** [all] Error 2

the blat executable in dependencies is for x86 machines. I tried to replace it with an arm64 version from conda but not work. Have you guys tried on a m1 Mac. Or is there a way to build myself?

I would like to try out Mirage but it seems that the build/install instructions and scripts may need updating. I should be able to setup the dependencies and may be able to put files in the right places manually but it may be worth fixing.

.

Outputs

Hello Mirage Team,
I would like to use your tool. I've downloaded genomes and gtf files by using your Download-Genomes.sh and Download-GTFs.sh scripts. I tried the tool for obscurin proteins with "./mirage2 obscn.fa species-guide.txt" command, however the Mirage-results/Final-MSAs directory contains only protein fasta files (unaligned). In each fasta file original protein sequence is stored. Species-MSAs/Misc/alignments directory contains same fasta files as well. Mappings directory is empty. Do I run the tool wrong? I appreciate your help. Thank you