search

Illumina / isaac2

Aligner for sequencing data
Other
21 stars 4 forks source link

Error occurs when isaac-unpack-reference #5

Closed zeus19900814 closed 9 years ago

zeus19900814 commented 9 years ago

Hi Come,

I was doing some testing trying to move around isaac reference files.

First I ran isaac-pack-reference -r /path/to/sorted-reference.xml and then I got packed-reference.tar.gz and a Temp directory which contains .16bpb.gz, a copy of original fasta, sorted-reference.xml and a .sentinel file.

Then how can I unpack the .tar.gz file to the target directory? I tried to run ./isaac-unpack-reference -i packed-reference.tar.gz but I got "../share/iSAAC-02.15.07.16/makefiles/reference/UnpackReferenceSubmake.mk:67: *\ "Expected 1 annotation path, got: ". Stop.". Am I missing something here?

I didn't see an example in the manual or an input option to specify the output directory.

Thank you, Ivan

come-raczy commented 9 years ago

Hi Ivan,

You are right, there isn't an option to specify the output directory. The reference will always be unpacked in the current directory. Make sure that the current directory does not contain a 'Temp' directory.

Thanks,

Come

On Monday, August 10, 2015, zeus19900814 notifications@github.com wrote:

Hi Come,

I was doing some testing trying to move around isaac reference files.

First I ran isaac-pack-reference -r /path/to/sorted-reference.xml and then I got packed-reference.tar.gz and a Temp directory which contains .16bpb.gz, a copy of original fasta, sorted-reference.xml and a .sentinel file.

Then how can I unpack the .tar.gz file to the target directory? I tried to run ./isaac-unpack-reference -i packed-reference.tar.gz but I got "../share/iSAAC-02.15.07.16/makefiles/reference/UnpackReferenceSubmake.mk:67: *\ "Expected 1 annotation path, got: ". Stop.".

I didn't see an example in the manual or an input option to specify the output directory.

Thank you, Ivan

— Reply to this email directly or view it on GitHub https://github.com/Illumina/isaac2/issues/5.