Categories
emacs Linux

Setup NCBI E-utilities

The E-utilities toolbox from NCBI is the recommended way to access NCBI and NLM data, including the genome data. The following command can easily install it in the Ubuntu Linux distribution.

$sudo apt update
$sudo apt install ncbi-entrez-direct

After successful installation you can test it out using the following example code, which provides ftp path to the first 10 Bacillus cereus in refseq. Unfortunately, this code needs to run in the BASH shell. Running it in eshell (within Emacs) does not work.

$esearch -db assembly -query "Bacillus cereus " | efetch -format docsum -mode json|grep "ftppath_refseq" |head -10
            "ftppath_refseq": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/394/245/GCF_013394245.1_ASM1339424v1",
            "ftppath_refseq": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/303/115/GCF_013303115.1_ASM1330311v1",
            "ftppath_refseq": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/284/505/GCF_013284505.1_ASM1328450v1",
            "ftppath_refseq": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/284/455/GCF_013284455.1_ASM1328445v1",
            "ftppath_refseq": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/284/445/GCF_013284445.1_ASM1328444v1",
            "ftppath_refseq": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/284/425/GCF_013284425.1_ASM1328442v1",
            "ftppath_refseq": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/267/775/GCF_013267775.1_ASM1326777v1",
            "ftppath_refseq": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/267/475/GCF_013267475.1_ASM1326747v1",
            "ftppath_refseq": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/267/455/GCF_013267455.1_ASM1326745v1",
            "ftppath_refseq": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/267/275/GCF_013267275.1_ASM1326727v1",

Categories
emacs

View PDF in Emacs

Be default PDF files are opened by Docviewer in Ubuntu distributes. Yet, there is a more convenient PDF tool, aptly named pdf-tools that works well with Emacs. The installation of pdf-tools is straight forward. Below is what I did.

sudo apt install libpng-dev zlib1g-dev
sudo apt install libpoppler-glib-dev
sudo apt install libpoppler-private-dev

After that, go to Emacs and use the package-install to install

package-refresh-contents
package-install pdf-tools

Finally, add the following line to the .emacs file. And make sure that if you are displaying line numbers in emacs, make sure it is disabled in pdf-view-mode. Here what I used is to just enable line number display in prog-mode.

(pdf-tools-install)
(add-hook 'prog-mode-hook 'linum-on)