Python client

Installation

1. LabxDB-tools depends on requests, urllib3 and pyfnutils Python modules. To install it and its dependencies:

   pip3 install labxdb-tools --user
   

2. Make sure $HOME/.local/bin is in your PATH; the script import_seq for example should be executable. If not, configure your PATH in your ~/.bashrc:

   export PATH=$PATH:$HOME/.local/bin
   

Dependencies

1. import_seq

   Install zstd, wget and squashfs-tools with your favourite package manager. For example:

   pacman -S zstd wget squashfs-tools
   

   Notesquashfs-tools is not mandatory. After download, remaining files can be (i) kept as-is or (ii) deleted using the option --delete_download.

2. import_sra

   Install fastq-dump from the NCBI SRA (Sequence Read Archive) tools:

   wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz
   tar xvfz sratoolkit.current-ubuntu64.tar.gz
   cp sratoolkit.*-ubuntu64/bin/fastq-dump-orig* $HOME/.local/bin/fastq-dump
   

Configuration

To access LabxDB databases, clients need URL, path, login and passwords. They can be provided as environment variables or in a configuration file.

By environment variables

In your '~/.bashrc:

export LABXDB_HTTP_URL="http://127.0.0.1:8081/"
export LABXDB_HTTP_PATH_SEQ="seq/"
export LABXDB_HTTP_LOGIN=""
export LABXDB_HTTP_PASSWORD=""

By configuration file

In any file within any of these folders:

• $HTS_CONFIG_PATH. HTS_CONFIG_PATH can be defined by the user.
• $XDG_CONFIG_HOME/hts. XDG_CONFIG_HOME is defined by your desktop environment.

Example configuration:

1. Create a folder /etc/hts
2. Open a file /etc/hts/labxdb.json and write (in JSON format):

   {
       "labxdb_http_url": "http://127.0.0.1:8081/",
       "labxdb_http_path_seq": "seq/",
       "labxdb_http_login": "",
       "labxdb_http_password": ""
   }
   

3. Open a file /etc/hts/path.json and write (in JSON format):

   {
       "path_seq_raw": "/data/seq/raw",
       "path_seq_run": "/data/seq/by_run",
       "path_seq_prepared": "/data/seq/prepared"
   }
   

4. Add in ~/.bashrc:

   export HTS_CONFIG_PATH="/etc/hts"