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Web content for Meren Lab

License: MIT License

Ruby 0.05% JavaScript 12.07% HTML 13.40% Python 11.49% Shell 0.39% Jupyter Notebook 39.68% R 9.24% SCSS 13.68%

merenlab.org's Introduction

Contributions welcome!

If you want to contribute to the web page, whether it is to fix something somewhere, or to write a blog post, there are two things you need to do.

The first is to be able to run the web page locally so you can see how things are rendered and how they will look online when you finally commit your changes to this repository. The remainder of this document will help you run the web site locally.

The second is to take a look at these tips which will help you to be able to use all the little toys we have for content developers:

https://merenlab.org/web-tips/

How to run a copy of this website locally

Installing ruby on Mac is always a pain. But you can start with this (newer versions of ruby may cause you trouble with some of the gems):

brew install [email protected]

This step may ask you to add things to your ~/.bash_profile to update your $PATH, which you should do, and then either open a new terminal, or run source ~/.bash_profile, so the output for which ruby looks something like this:

/usr/local/opt/[email protected]/bin/ruby

Once you're done with these initial steps, you can get a copy of the web site from GitHub:

mkdir -p ~/github
cd ~/github/

git clone https://github.com/merenlab/web.git

To make sure you have the necesary gems, run:

cd web
bundle install

And run the following command in this directory:

bundle exec jekyll serve --incremental

You should see a similar output in your terminal:

Configuration file: /Users/evan/Software/web/_config.yml
Configuration file: /Users/evan/Software/web/_config.yml
            Source: /Users/evan/Software/web
       Destination: /Users/evan/Software/web/_site
 Incremental build: enabled
      Generating...
                    done in 6.585 seconds.
 Auto-regeneration: enabled for '/Users/evan/Software/web'
Configuration file: /Users/evan/Software/web/_config.yml
    Server address: http://127.0.0.1:4000/
  Server running... press ctrl-c to stop.

This basically runs a local server for you to see the changes you've made locally. You can access to this server by visiting the URL http://127.0.0.1:4000/ with your browser.

With the --incremental flag every change you will make in any of the files will be reflected to your local website automatically.

If you are not seeing some of the changes you expect to see, press ctrl-c to stop the server on your termianl, clean out the static web directory by running the command rm -rf _site/, and re-run the server using the command above.

How to get yourself fired from the lab

It is simple.

You can make the following changes in the web site:

find ./_posts/ -type f | xargs sed -i '' -e  "s/An anvi'o/A microbial dark matter \(MDM\)/g"
find ./_posts/ -type f | xargs sed -i '' -e  "s/an anvi'o/a microbial dark matter \(MDM\)/g"
find ./_posts/ -type f | xargs sed -i '' -e  "s/Anvi'o/Microbial dark matter \(MDM\)/g"
find ./_posts/ -type f | xargs sed -i '' -e  "s/anvi'o/microbial dark matter \(MDM\)/g"
find ./_posts/ -type f | xargs sed -i '' -e  "s/anvi'o/microbial dark matter \(MDM\)/g"
find ./_posts/ -type f | xargs sed -i '' -e  "s/anvi'server/MDM'server/g"

And commit them to the main repository after making sure they look alright in your local copy:

git add .
git commit -m "name upgrade"
git push origin master

Congratulations!

merenlab.org's People

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merenlab.org's Issues

error in gff_parser.py

Dear Sir,
Followed the instruction of 'web/_posts/anvio/2017-05-18-working-with-prokka.md' at https://github.com/merenlab/web/blob/master/_posts/anvio/2017-05-18-working-with-prokka.md, and run

 python gff_parser.py prokka/sample.gff --gene-calls gene_calls.txt --annotation gene_annot.txt

I got an error of gff_parser.py which appears in line 43 as:

File "gff_parser.py", line 43, in <module>
    source, version = feature.source.split(':')
ValueError: not enough values to unpack (expected 2, got 1)

Could you please take a look at that? Thank you.

Are hyperlinks hard to see?

Color is a subjective thing, especially with the prominence of color blindness in our population. What pops to some may be invisible to others.

So I wanted to ask, does anyone else feel these hyperlinks are difficult to see? On a 1-10 scale of visibility, I would rank these as a 2:

Especially given the visual prominence of our new artifact hyperlinks (green), I fear from my own experience that our hyperlinks are being looked over by readers.

minor blog issues

I came up with a couple of minor outdated stuff in some of the blog pages and wanted to let you know.

For each page, I listed the issues that I came up with: Related lines within the page in quotes and the issue in bold.

1) https://merenlab.org/2019/11/25/visualizing-coverages/

“For this summary we have extensively relied upon this video” (video does not work)
“If you’d like to download the necessary anvi’o files to follow this post, please feel free to download them from here” (link does not work)

Profile DB was outdated, so I migrated it to v37 (tried with both safe and quick modes) but then I got the following issue when I run anvi-interactive:

Config Error: Oh no :( There is a contigs database here at 'CONTIGS.db', but it seems to be
broken :( It is very likely that the process that was trying to create this
database failed, and left behind this unfinished thingy (if you would like to
picture its state you should imagine the baby Voldemort at King's Cross). Well,
anvi'o believes it is best if you make it go away with fire, and try whatever
you were trying before you got this error one more time with a proper contigs
database. End of sad news. Bye now.

2) https://merenlab.org/tutorials/assembly-based-metagenomics/

“If you would like to change something on this page, you can directly edit its source code” (link does not work)

3) https://merenlab.org/tutorials/infant-gut/#chapter-i-genome-resolved-metagenomics

“There is also a step-by-step workflow to describe steps of manual curation here.” (link does not work)
“Centrifuge (code, pre-print) is one of the options to....” (Centrifuge is not a pre-print anymore)
“But once we are done with this, please see the relevant section in this study.” (This is also not a pre-print, link should be updated)

4) https://merenlab.org/2017/06/07/phylogenomics/

“The first thing we need to do is to generate an anvi’o contigs database for each one of them:” (Contigs db for two of the .fa files cannot be created - Salmonella_enterica_21806 and Escherichia_coli_9038. Solved by anvi-script-reformat-fasta Escherichia_coli_9038.fa --seq-type NT -o Escherichia_coli_9038_fixed.fa):

Config Error: Tough. Escherichia_coli_9038_contig_00002_plasmid contains characters that are
not any of A, C, T, G, N, a, c, t, g, n. To save you from later headaches,
anvi'o will not make a database. We recommend you identify what's up with your
sequences. If you want to continue, first reformat the FASTA file (you could use
anvi-script-reformat-fasta with the parameter --seq-type NT, and that would fix
the problem)

5) https://merenlab.org/data/prochlorococcus-metapangenome/

“The URL http://merenlab.org/data/prochlorococcus-metapangenome serves the most up-to-date version of this document.” (URL does not work, the link seems to be wrong)

Ncbi-genome-download

Hi, I was trying to download the genome for NCBI using ncbi-genome-download, When I ran the anvi-script-process-genbank-metadata script, I got the genomes, but they are not the same size as those in the database. I wanted to know why there is a difference in size. Can you help?

Remaining discrepancies `A primer on anvi'o`

Collection of discrepancies I noticed between the tutorial (after Mete's updates) and my outputs. I'll write one comment per issue as I notice them.

ToC cursor

In long documents like the infant gut tutorial, the ToC itself can become very disorienting. It would be great to have some cursor or highlight that indicates where the user's current scrollview is.