Commit 897a8148 authored by Sascha Steinbiss's avatar Sascha Steinbiss
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New upstream version 2.13.2+ds

parent 60af3c31

CHANGELOG.md

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README.md

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@@ -60,7 +60,7 @@ Please read the [ARIBA wiki page][ARIBA wiki] for full usage instructions. 
If you encounter an issue when installing ARIBA please contact your local system administrator. If you encounter a bug please log it [here](https://github.com/sanger-pathogens/ariba/issues) or email us at ariba-help@sanger.ac.uk.



### Required dependencies

  * [Python3][python] version >= 3.3.2

  * [Python3][python] version >= 3.4.0

  * [Bowtie2][bowtie2] version >= 2.1.0

  * [CD-HIT][cdhit] version >= 4.6

  * [MUMmer][mummer] version >= 3.23
@@ -73,6 +73,7 @@ are not already installed: 
  * pyfastaq >= 3.12.0

  * pysam >= 0.9.1

  * pymummer >= 0.10.1

  * biopython



### Using pip3

Install ARIBA using pip:

ariba/tb.py

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@@ -212,8 +212,8 @@ def write_prepareref_metadata_file(mutations, outfile): 


def make_prepareref_files(outprefix):

    genbank_file = os.path.join(data_dir, 'NC_000962.3.gb')

    mut_to_drug_json = os.path.join(data_dir, 'panel.20181115.json')

    panel_txt_file = os.path.join(data_dir, 'panel.20181115.txt')

    mut_to_drug_json = os.path.join(data_dir, 'panel.20181221.json')

    panel_txt_file = os.path.join(data_dir, 'panel.20181221.txt')

    fasta_out = outprefix + '.fa'

    tsv_out = outprefix + '.tsv'

ariba/tb_data/panel.20181221.json

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ariba/tb_data/panel.20181221.txt

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