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a2iEditing / RNAEditingIndexer

A tool for the calculation of RNA-editing index for RNA seq data
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Docker permissions GenerateIndex #9

Closed AMChalkie closed 4 years ago

AMChalkie commented 4 years ago

Hi,

I'm seeing the following failure on index generation. I suggest Suggest adding the .fai to the docker resource download.

/Alistair

GenerateIndex - Starting! Running: bedtools getfasta -name -bedOut -fi '/bin/AEI/RNAEditingIndexer/Resources/Genomes/MusMusculus/ucscMm10Genome.fa' -bed '/bin/AEI/RNAEditingIndexer/Resources/Regions/MusMusculus/ucscMM10SINE_B1_B2.bed.gz' GenerateIndex - Indexing FASTA Records! GenerateIndex - encountered unexpected line from bedtools, skipping line. Line:index file /bin/AEI/RNAEditingIndexer/Resources/Genomes/MusMusculus/ucscMm10Genome.fa.fai not found, generating... GenerateIndex - encountered unexpected line from bedtools, skipping line. Line:could not open index file /bin/AEI/RNAEditingIndexer/Resources/Genomes/MusMusculus/ucscMm10Genome.fa.fai for writing! GenerateIndex - getfasta Failed! Empty Output was Found

AMChalkie commented 4 years ago

Solution: Add this to Dockerfile: (once for each genome.fa) RUN samtools faidx /bin/AEI/RNAEditingIndexer/Resources/Genomes/MusMusculus/ucscMm10Genome.fa

shalomhillelroth commented 4 years ago

Hi, Thanks!

I'm working on a quick patch (to solve the configuration problems on different OS, using autoconf), hopefully in the next couple days I'll finish testing it. I will add your suggestion, but to the initialization script (obviously with credit).

Best,

Shalom Hillel Roth