Codebase list barrnap / 10c6a5b
Add conda install instructions Torsten Seemann 6 years ago
1 changed file(s) with 23 addition(s) and 13 deletion(s). Raw diff Collapse all Expand all
1818 NHMMER binaries for 64-bit Linux and Mac OS X are included and will be auto-detected.
1919 Multithreading is supported and one can expect roughly linear speed-ups with more CPUs.
2020
21 ## Download
21 ## Installation
2222
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):
2525
26 ## Install
26 conda -c bioconda install barrnap
27 barrnap --version
2728
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
3242
3343 ## Usage
3444
3545 % barrnap --quiet examples/small.fna
3646 ##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
4050
4151 % barrnap -q -k mito examples/mitochondria.fna
4252 ##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
4555
4656 ## Caveats
4757