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milaboratory / mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
https://mixcr.com
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Error running importFromIMGT #106

Closed KestindotC closed 8 years ago

KestindotC commented 8 years ago

Hello, I think there might be pup error in these message, but how could I fix it?

$ mixcr importFromIMGT Starting importFromIMGT.sh script By using this script you agree to the terms of use of IMGT website. (see http://www.imgt.org/ for details). Press ENTER to continue or other key to exit... ~/.linuxbrew/Cellar/mixcr/1.7-5/importFromIMGT.sh: line 40: ~/.linuxbrew/bin/pup: cannot execute binary file: Exec format error Available species: Please select species (e.g. '5' for ): ......

So I was wondering if any of solution to solve this problem? Thanks!

dbolotin commented 8 years ago

Yap, there is a known issue with pup installed using linuxbrew.

Here is the solution:

  1. Unlink pup installed using brew:

    brew unlink pup

  2. Setup environment for go:

    mkdir ~/.go

    add the following lines to your .bashrc (or equivalent file):

    export GOPATH="$HOME/.go"
export PATH="$HOME/.go/bin:$PATH"

  3. Relogin to the shell and install pup using go get:

    go get github.com/ericchiang/pup
KestindotC commented 8 years ago

Thanks for the reply!! go get work ~

dbolotin commented 8 years ago

Good!