search

thelovelab / tximeta

Transcript quantification import with automatic metadata detection
https://thelovelab.github.io/tximeta/
66 stars 11 forks source link

Bioconda version still 1.6.2 #47

Closed matmu closed 3 years ago

matmu commented 3 years ago

I would like to add tximeta to my Docker container by installing it via Conda. The version in Bioconda is still 1.6.2 (https://anaconda.org/bioconda/bioconductor-tximeta), although there is already the more recent version 1.6.3 available. With 1.6.2 I am facing problems to automatically recognize the transcriptome I am using. Could you please update it to 1.6.3 or tell me who I have to approach? Thanks a lot.

mikelove commented 3 years ago

This is outside of my scope (I don't maintain the bioconda versions).

One solution is that you could add the transcriptome you are using via makeLinkedTxome(). It's just one function call and then your transcriptome will be recognized and tximeta functions will work as if you were using 1.6.3.

matmu commented 3 years ago

@mikelove Thanks for your help. I was able to update the bioconda version of tximeta myself today. I am already using makeLinkedTxome() as a workaround. Is there any speed difference between makeLinkedTxome() and the automated mode?

mikelove commented 3 years ago

No speed difference, tximeta is doing a few things: read in the data with tximport, lookup the checksum in the table to find a match, compile the metadata (which may involve possibly downloading and possibly parsing a file, or using a cached version of the file or database), packaging the output.