Comments (2)
andrewjpage
commented on August 14, 2024
Hi Nadejda,
It looks like the dependancies are not all installed. Most likely the issue is with bedtools. If you checkout the code from github then run the tests, they should pass.
https://github.com/sanger-pathogens/Roary/blob/master/
In particular if you run:
perl t/00_requires_external.t
it will check for the dependancies.
The recommended method of installation is using LinuxBrew or HomeBrew.
Regards,
Andrew
from roary.
andrewjpage
commented on August 14, 2024
version 3.2.9 now includes an option to check the dependancies which will make issues like this easier to detect. Functionality in pull request #180
from roary.
Related Issues (20)
- number of conserved/unique genes.Rtab
- Strange Ouput HOT 2
- Number of conserved genes increases through genomoes
- how can i solve this issue
- No newick file
- Missing proteome.faa files
- Cant open file: 14L9VpZJtx/DNA16.gff.proteome.faa Please, help with this issue
- roary_plots.py heatmap coregenome matrix empty
- i cant install Roary by mamba HOT 2
- core_alignment.aln has lower and uppercase in sequences
- cann't install roary 3.13 with mamba/conda
- The singularity image pulled from docker://sangerpathogens/roary does not accept input gff files HOT 2
- Issue with "Error: Cant access the groups file: clustered_proteins" HOT 1
- How can I discover the genetic sequences that are used to group groups in roary?
- Roary grouping genes that don't meet similarity threshold (using `-i 100`, and `-s`) HOT 6
- Order of genes in alignment
- Use of uninitialized value in require at /usr/lib/x86_64-linux-gnu/perl5/5.34/Encode.pm line 70.
- How are genes with frameshift mutations/INDELS handled?
- The number of pan-genes in gene_presence_absence.csv is less than each genome
- Cloud not obtain clear phylogenic tree HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from roary.