changed 3 years ago
Linked with GitHub

asgal - user installation @UPPMAX

Documentation: https://asgal.algolab.eu/documentation

Installation instuctions

Note: compiling the code and the prerequisites might take some time, so an interactive job might be needed for the purpose of the installation.

# load python from the module system
$ module load python/3.7.2

# make virual environment in your project folder 
$ cd /proj/project_folder
$ python3 -m venv asgal
# activate the environment
$ source asgal/bin/activate
$(asgal) pip install -U pip setuptools wheel  # some updates as precaution

# Follow the install instructions 
$(asgal) git clone --recursive https://github.com/AlgoLab/galig.git
$(asgal) cd galig
$(asgal) make prerequisites
$(asgal) make 

# FIX the python3 call
# Edit the `asgal` file and replace the first line with "#!/usr/bin/env python3"

# install some missing modules (might need more)
$(asgal) pip install Bio pysam pandas

# test
$(asgal) ./asgal -h
usage: asgal [-h] -g REFPATH -a ANNOPATH -s SAMPLE1PATH -o OUTPUTPATH
             [-s2 SAMPLE2PATH] [-t TRANSPATH] [-l L] [-e E] [-w W]
             [--allevents] [--multi] [--verbose] [--debug] [--split-only]
             [-@ THREADS]

ASGAL - Alternative Splicing Graph ALigner

optional arguments:
  -h, --help            show this help message and exit
  -g REFPATH, --genome REFPATH
                        Path to genome (default: None)
  -a ANNOPATH, --annotation ANNOPATH
                        Path to annotation (default: None)
  -s SAMPLE1PATH, --sample SAMPLE1PATH
                        Path to sample (1) (default: None)
  -o OUTPUTPATH, --output OUTPUTPATH
                        Path to output folder (default: None)
  -s2 SAMPLE2PATH, --sample2 SAMPLE2PATH
                        Path to sample (2) (default: -)
  -t TRANSPATH, --transcripts TRANSPATH
                        Path to transcripts (default: -)
  -l L, --L L           MEMs length (default: 15)
  -e E, --erate E       Error rate (default: 3)
  -w W, --support W     Minimum intron coverage (default: 3)
  --allevents           Use this if you want to detect all events, also
                        annotated ones (default: False)
  --multi               Use this to run ASGAL in genome-wide mode (default:
                        False)
  --verbose             Add some prints to stderr (default: False)
  --debug               Add debug prints to stderr (default: False)
  --split-only          Only split files per gene, do not run ASGAL (default:
                        False)
  -@ THREADS, --threads THREADS
                        Number of threads to use for salmon mapping and
                        parallel gene computation (default: 2)

Running after installaltion

# load python
$ module load python/3.7.2
# activate the environment
$ source asgal/bin/activate
$(asgal) cd galig

# run
$(asgal) ./asgal ...


Only for reference purposes

pip list
$(asgal) pip list
Package            Version
------------------ ---------
argcomplete        1.12.2
argh               0.26.2
bio                0.2.4
biopython          1.78
certifi            2020.12.5
chardet            4.0.0
gffutils           0.10.1
idna               2.10
importlib-metadata 3.3.0
numpy              1.19.4
pandas             1.1.5
pip                20.3.3
pyfaidx            0.5.9.2
pysam              0.16.0.1
python-dateutil    2.8.1
pytz               2020.4
requests           2.25.1
setuptools         51.0.0
simplejson         3.17.2
six                1.15.0
typing-extensions  3.7.4.3
urllib3            1.26.2
wheel              0.36.2
zipp               3.4.0

Contacts:


tags: UPPMAX, SNIC, RT-222892
Select a repo