Add conda install instructions
Torsten Seemann
6 years ago
18 | 18 | NHMMER binaries for 64-bit Linux and Mac OS X are included and will be auto-detected. |
19 | 19 | Multithreading is supported and one can expect roughly linear speed-ups with more CPUs. |
20 | 20 | |
21 | ## Download | |
21 | ## Installation | |
22 | 22 | |
23 | * Tarballs: https://github.com/tseemann/barrnap/releases/ | |
24 | * Source: https://github.com/tseemann/barrnap | |
23 | ### Conda | |
24 | Install [Conda](https://conda.io/docs/) or [Miniconda](https://conda.io/miniconda.html): | |
25 | 25 | |
26 | ## Install | |
26 | conda -c bioconda install barrnap | |
27 | barrnap --version | |
27 | 28 | |
28 | % cd $HOME | |
29 | % tar zxvf barrnap-0.X.tar.gz | |
30 | % echo "PATH=$PATH:$HOME/barrnap-0.x/bin" >> .bashrc | |
31 | (logout and log back in) | |
29 | ### Homebrew | |
30 | Install [HomeBrew](http://brew.sh/) (Mac OS X) or [LinuxBrew](http://brew.sh/linuxbrew/) (Linux). | |
31 | ||
32 | brew tap brewsci/bio | |
33 | brew install barrnap | |
34 | barrnap --help | |
35 | ||
36 | ### Source | |
37 | This will install the latest version direct from Github. You'll need to add the ```bin``` directory to your PATH. | |
38 | ||
39 | cd $HOME | |
40 | tar zxvf barrnap-0.X.tar.gz | |
41 | barrnap-0.X/barrnap -h | |
32 | 42 | |
33 | 43 | ## Usage |
34 | 44 | |
35 | 45 | % barrnap --quiet examples/small.fna |
36 | 46 | ##gff-version 3 |
37 | P.marinus barrnap:0.7 rRNA 353314 354793 0 + . Name=16S_rRNA;product=16S ribosomal RNA | |
38 | P.marinus barrnap:0.7 rRNA 355464 358334 0 + . Name=23S_rRNA;product=23S ribosomal RNA | |
39 | P.marinus barrnap:0.7 rRNA 358433 358536 7.5e-07 + . Name=5S_rRNA;product=5S ribosomal RNA | |
47 | P.marinus barrnap:0.8 rRNA 353314 354793 0 + . Name=16S_rRNA;product=16S ribosomal RNA | |
48 | P.marinus barrnap:0.8 rRNA 355464 358334 0 + . Name=23S_rRNA;product=23S ribosomal RNA | |
49 | P.marinus barrnap:0.8 rRNA 358433 358536 7.5e-07 + . Name=5S_rRNA;product=5S ribosomal RNA | |
40 | 50 | |
41 | 51 | % barrnap -q -k mito examples/mitochondria.fna |
42 | 52 | ##gff-version 3 |
43 | AF346967.1 barrnap:0.7 rRNA 643 1610 . + . Name=12S_rRNA;product=12S ribosomal RNA | |
44 | AF346967.1 barrnap:0.7 rRNA 1672 3228 . + . Name=16S_rRNA;product=16S ribosomal RNA | |
53 | AF346967.1 barrnap:0.8 rRNA 643 1610 . + . Name=12S_rRNA;product=12S ribosomal RNA | |
54 | AF346967.1 barrnap:0.8 rRNA 1672 3228 . + . Name=16S_rRNA;product=16S ribosomal RNA | |
45 | 55 | |
46 | 56 | ## Caveats |
47 | 57 |