ILRI Research Computing

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====== sistr ======
Serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST. Mash MinHash can also be used for serovar prediction.

  * Latest Version: 1.0.2
  * Added: January, 2018
  * Link: https://github.com/peterk87/sistr_cmd

===== Usage =====
Show all available versions of sistr:

<code>$ module avail sistr</code>

Load a particular version of sistr and run it:

<code>$ module load sistr/1.0.2
$ sistr -h</code>

===== Installation =====
Notes from the sysadmin during installation:

<code>$ module load python/3.6.2
$ sudo mkdir -p /export/apps/sistr/1.0.2
$ sudo chown aorth /export/apps/sistr/1.0.2
$ python -m venv /export/apps/sistr/1.0.2
$ . /export/apps/sistr/1.0.2/bin/activate
$ pip install --upgrade pip
$ pip install wheel
$ pip install numpy pandas
$ pip install sistr_cmd
$ sudo chown -R root:root /export/apps/sistr/1.0.2</code>