"Uncompressing db failed" superfocus_downloadDB.py blast

[Mark Bashir Hamidi]

Getting the below error due to superfocus_downlaodDB.py not finding the downloaded db.

(super-focus) [x@y ~]$ superfocus_downloadDB.py blast
Downloading DB
--2018-07-13 14:40:58-- http://edwards.sdsu.edu/superfocus/downloads/db.zip
Resolving edwards.sdsu.edu... 130.191.93.70
Connecting to edwards.sdsu.edu|130.191.93.70|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3527705740 (3.3G) [application/zip]
Saving to: "db.zip"

100%[=======================================================================================>] 3,527,705,740 39.3M/s in 49m 22s

2018-07-13 15:30:20 (1.14 MB/s) - "db.zip" saved [3527705740/3527705740]

Uncompressing DB
unzip: cannot find or open db/db.zip, db/db.zip.zip or db/db.zip.ZIP.
mv: accessing db/': Not a directory rm: cannot remove db/db.zip': Not a directory

Joining files
Traceback (most recent call last):
File "/home/bah29/packages/anaconda3/envs/super-focus/bin/superfocus_downloadDB.py", line 119, in
main()
File "/home/bah29/packages/anaconda3/envs/super-focus/bin/superfocus_downloadDB.py", line 108, in main
donwloadDBnFormat(aligners)
File "/home/bah29/packages/anaconda3/envs/super-focus/bin/superfocus_downloadDB.py", line 46, in donwloadDBnFormat
for cluster in os.listdir("db/clusters/")
OSError: [Errno 20] Not a directory: 'db/clusters/'

The db is still accessible in the downloaded directly. I have unzipped db as such:
(super-focus) [x@y ~]$ unzip "db" -d db2/
Do I need to move the unzipped db to a particular directory?

[Geni Silva]

we have been working to move the tool into bioconda, and it looks like the download script is not working correctly when installing the tool with conda.

quick solution: cd /home/bah29/packages/anaconda3/envs/super-focus/bin/ (which i believe is where conda put the super-focus scripts) and then superfocus_downloadDB.py blast

I will work on the fix in the mean time - sorry about that.