I'm interested in using Cufflinks with reference annotation on my local Galaxy instance. I'm wondering how I can install reference annotation to my local Galaxy so that it's available to all the user? I tried searching for data_manager in the tool shed but I don't see such tool for fetching reference annotation.
I also tried downloading a reference annotation from the link provided on the Cufflinks website. I downloaded the UCSC version using the Get Data interface provided by Galaxy. I had this error:
Fatal error: Exit code 1 () Error running cufflinks. return code = 1 Command line: cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 -G /home/joe/galaxy/database/files/000/dataset_25.dat /home/joe/galaxy/database/files/000/dataset_13.dat [16:34:05] Loading reference annotation. Error parsing strand (3) from GFF line: uc007aeu.1 chr1 - 3204562 3661579 3206102 3661429 3 3204562,3411782,3660632, 3207049,3411982,3661579, Q5GH67 uc007aeu.1