guide.txt

- Sequenceserver - BLAST

General docs is available here: https://sequenceserver.com/doc/

Sequenceserver has it own user in the server

The configuration file is located in /home/sequenceserver/.sequenceserver.conf

In order to know where sequenceserver is installed, logged as the proper user run:

echo "$(ruby -e 'puts Gem.path[0]')/gems/sequenceserver-2.1.0"

To the databases available:

sequenceserver --list_databases

There is a systemd autostart script in /etc/systemd/system/sequenceserver.service 
The content of the script is the following:

```
[Unit]
Description=SequenceServer server daemon
Documentation="file://sequenceserver --help" "http://sequenceserver.com/doc"
After=network.target

[Service]
Type=simple
User=sequenceserver
ExecStart=/usr/local/ruby-3.2.2/bin//sequenceserver -c /home/sequenceserver/.sequenceserver.conf
KillMode=process
Restart=on-failure
RestartSec=42s
RestartPreventExitStatus=255

[Install]
WantedBy=multi-user.target
```

-- Adding new databases

Add the fasta file to /Databig/BLAST_DBs

Stop the seqeunceserver

  service sequenceserver stop

and format the DBs:

  ~/.sequenceserver/ncbi-blast-2.12.0+/bin/makeblastdb  -in /DataBig/BLAST_DBs/file.fasta -dbtype prot -title 'DB title'

Restart the sequenceserver

  service sequenceserver start

Alternatively database could be formated with (after adding the fasta file to the proper path)

  sequenceserver --make-blast-databases

However this uses the 'parse_seqids' option of makeblastdb, which will fail if the DB identifiers are larger than 50 chars.

In order to add links to blast results add the proper code here:

  /usr/local/ruby-3.2.2/lib/ruby/gems/3.2.0/gems/sequenceserver-2.1.0/lib/sequenceserver/links.rb

- Website LabBCES
-- Installing HUGO

For this version of the website we need hugo 0.84.4 and go https://github.com/gohugoio/hugo
Get hugo from :
Install golang in ubuntu as:
apt install golang-go

-- Adding new people

--- Edditing people
People info are under content/authors, for each person there is a folder in that path. Edit the _index.md file and the avatar.jpg|png to have a pic.

-- Adding publications
Add publication into the bib file (using JabRef): biblioDMRP.bib
And then run:

academic import --bibtex biblioDMRP.bib

If previous publication had been updated tne overwrite the import with the flag --overwrite

academic import --overwrite --bibtex biblioDMRP.bib

#new versios of the academic tool have conflick with hugo 0.84.4. If after adding a new publication the hugo compilation fails with an error regarding article-journal not bein an integer, just change the tak article-journal to number 2 in the index.md of the new publication

-- Adding news

in the root folder of the site run:

hugo new --kind post post/25-11-2021-BSB2021

then edit the index.md file

-- Adding projects

hugo new  --kind project project/my-project-name
#https://wowchemy.com/docs/content/projects/

-- Adding events
hugo new  --kind event event/SAGB-26042023
#For instance our seminario de afinidades

-- Add a picture to the film roll

Add the jpeg file to content/pictures/bces/
Add description in content/pictures/index.md


-- Adding slides

hugo new --kind slides slides/SAGB-30082023/

-- Adding a new item to the top menu

Edit the file config/_default/menus.yaml

#Example hugo new --kind slides slides/SAGB-30082023/
# Doc for example hugo new --kind slides slides/SAGB-30082023/
#Doc https://wowchemy.com/docs/content/slides/

-- Deploy website

#In order to deploy the website in opur server labbces.cena.usp.br, we need to use hugo version 0.84.4, the latest version do not work with the templates from wowchemy
hugo --gc --minify -b http://labbces.cena.usp.br/
#and the copy to the server, which is already configure to serve from /home/labbces/www/

hugo --gc --minify -b http://labbces.cena.usp.br/
rsync -avz -e 'ssh -p 2222' public/ labbces@labbces.cena.usp.br:~/www/