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metageni / SUPER-FOCUS

A tool for agile functional analysis of shotgun metagenomic data

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Error when running download_DB command - wget command

vinisalazar opened this issue · comments

commented

Hi,

I was trying to use your program. I installed all the dependencies and had both blast and diamond installed. However, when I ran the superfocus_downloadDB -a <aligner> command for either aligner, I got an error, and the cause for it was not having wget installed.

I'm installing SUPER-FOCUS on a Mac computer, therefore wget is not installed by default. The default command for downloading in OS X is curl.

My problem was easily solved by installing wget command with brew.

However, to prevent this problem to future Mac users, I see some potential solutions:

  1. replacing wget with curl in the superfocus_downloadDB script.
  2. adding a statement like sys.platform or os.uname() to check the operating system and use the appropriate command.
  3. Incrementing the error message to say something like "Do you have wget installed? If not, you can install it with brew." (Least recommended).

I'd be happy to contribute with a PR for that.

I also submitted #19 which should help with installation.

bw,

V

commented

@vinisalazar thanks for the suggestion. I will include it in the next release.

commented

@vinisalazar I have merged the suggested changes. Thanks!

commented

happy to help. I hope to make time for further contributions even if they are just issues 🙂