-
Notifications
You must be signed in to change notification settings - Fork 3
/
Copy pathrequirements.txt
21 lines (20 loc) · 2.72 KB
/
requirements.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
1. [Python](https://www.python.org/) (version >= 3.6, requiring numpy, pandas, scipy packages; tested 3.6, 3.7)
2. [AnADAMA2](https://huttenhower.sph.harvard.edu/anadama2) (version >= 0.7.4; tested 0.7.4, 0.8.0)
3. [CD-hit](http://weizhongli-lab.org/cd-hit/) (version >= 4.7; tested 4.7)
4. [Diamond](http://www.diamondsearch.org/index.php) (version >= 0.9.24; tested 0.9.24)
5. [MSPminer](https://www.enterome.com/downloads/) (version >= 1.0.0; licensed software; tested version 1.0.0)
6. [MaAsLin2](https://huttenhower.sph.harvard.edu/maaslin2) (version >= 1.5.1; tested 1.5.1)
7. [Interproscan](https://interproscan-docs.readthedocs.io/en/latest/) (version >= 5.31-70) (installing with activating Phobius/SignalP/TMHMM analyses; InterProScan 5.51-85.0 or later are recommended for potential simpler installation; used for domain/motif annotation; tested 5.31-70, 5.51-85.0)
8. [Signalp](http://www.cbs.dtu.dk/services/SignalP-4.1/) (version >= 4.1; licensed software; installing with integrating in interproscan; used for domain/motif annotation; tested 4.1)
9. [TMHMM](http://www.cbs.dtu.dk/services/TMHMM/) (version >= 2.0; licensed software; installing with integrating in interproscan; used for domain/motif annotation; tested 2.0)
10. [Phobius](http://phobius.sbc.su.se/) (version >= 1.01; licensed software; installing with integrating in interproscan; used for domain/motif annotation; tested 1.01)
11. [PSORTb](https://psort.org/documentation/index.html) (version >= 3.0) (licensed software; used for domain/motif annotation; tested 3.0)
12. Optional: only required if using MetaWIBELE utilities to prepare inputs for MetaWIBELE using metagenomic sequencing reads
- [MEGAHIT](https://github.com/voutcn/megahit) (version >= 1.1.3; tested 1.1.3)
- [Prokka](https://github.com/tseemann/prokka) (version >= 1.14-dev; recommend to not set '-c' parameter when running prodigal with metagenome mode; tested 1.14-dev)
- [Prodigal](https://github.com/hyattpd/Prodigal) (version >= 2.6; tested 2.6)
- [USEARCH](http://www.drive5.com/usearch/) (version >= 9.0.2132; licensed software; tested 9.0.2132)
- [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) (version >= 2.3.2; tested 2.3.2)
- [SAMtools](https://github.com/samtools/) (version >= 1.9; tested 1.9)
- [featureCounts](http://bioinf.wehi.edu.au/featureCounts/) (version >= 1.6.2; tested 1.6.2)
Note: Please install the required software in a location in your `$PATH`. If you always run with gene families (non-redundant gene catalogs), the optional softwares are not required. Also if you always run with one or more bypass options (for information on bypass options, see optional arguments to the section in the User Manual. The software required for the steps you bypass does not need to be installed.