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INSTALL_DB deleted 100755 → 0
View file @ a77d84ce
#!/bin/bash
# INPUT: path_to_db
# Check if the user provided the input
if [ -z "$1" ]; then
echo "Provide a path to or a name for the database, followed by [ENTER]:"
read path
else
path=$1
fi
# Check if the path is valid and unexisting
if [ ! -d $path ]; then
git clone git@bitbucket.org:genomicepidemiology/resfinder_db.git $path
else
echo "Error: path exists! Please provide a valid and unused path..."
fi
echo "Do you want to fix permissions, yes/y or no/n, followed by [ENTER]:"
read fix
if [[ $fix == "yes" ]] || [[ $fix == "y" ]]; then
echo "enter group name followed by [ENTER]:"
read gn
if [ ! -z "$gn" ]; then
chgrp -R $gn $path
fi
find $path \( -name .git \) -prune -printf '' -o -type d -print -exec chmod 775 {} \;
find $path \( -name .git \) -prune -printf '' -o -type f -print -exec chmod 664 {} \;
fi
Makefile deleted 100755 → 0
View file @ a77d84ce
install:
cpanm CJFIELDS/BioPerl-1.6.924.tar.gz --force
cpanm Data::Dumper
cpanm Getopt::Long
cpanm File::Temp
clean:
find ./ -name "*.DS_Store" -delete
find ./ -name "*.log" -delete
find ./ -name "*.gz" -delete
README.md
View file @ 48318920
===================
ResFinder
===================
This project documents ResFinder service
Documentation
ResFinder documentation
=============
## What is it?
The ResFinder service contains one perl script *resfinder.pl* which is the
script of the latest version of the ResFinder service. ResFinder identifies
acquired antimicrobial resistance genes in total or partial sequenced isolates
of bacteria.
This repository also contains a python script *resfinder.py* which is a new version
of ResFinder, but not yet running on the CGE server. This program was added because
it uses a newer version of blastn, which, in contrary from the blastall version
that the perl script uses, is avail to download.
## Content of the repository
1. resfinder.pl - the program
2. INSTALL_DB - shell script for downloading the ResFinder database
3. UPDATE_DB - shell script for updating the database to the newest version
4. VALIDATE_DB - python script for verifying the database contains all
required files
5. brew.sh - shell script for installing dependencies
6. makefile - make script for installing dependencies
7. test.fsa - test fasta file
2. resfinder.py - (same program using an available blastn version - blastn-2.2.26+)
3. test.fsa - test fasta file
## Installation
Setting up ResFinder
Setting up ResFinder script and database
```bash
# Go to wanted location for resfinder
cd /path/to/some/dir
# Clone and enter the resfinder directory
git clone https://bitbucket.org/genomicepidemiology/resfinder.git
git clone https://git@bitbucket.org/genomicepidemiology/resfinder.git
cd resfinder
```
Installing up the ResFinder database
```bash
cd /path/to/resfinder
./INSTALL_DB database
# Check all DB scripts works, and validate the database is correct
./UPDATE_DB database
./VALIDATE_DB database
```
# Installing up the ResFinder database
# Go to wanted location for resfinder database
cd /path/to/some/dir
# Clone and enter the resfinder directory
git clone https://git@bitbucket.org/genomicepidemiology/resfinder_db.git
cd resfinder_db
Installing dependencies:
Perlbrew is used to manage isolated perl environments. To install it run:
```bash
bash brew.sh
```
This will installed Perl 5.23 in the Home folder, along with CPAN minus as
package manager.
Blast will also be installed when running brew.sh if BlastAll and FormatDB are
not already installed and place in the user's path.
After running brew.sh and installing Blast add this command to the end of your
~/bash_profile to add BlastAll and FormatDB to the user's path
### Installing dependencies (for python script):
```bash
export PATH=$PATH:blast-2.2.26/bin
```
The BlastAll and FormatDB that the perl script uses are no longer available
for downloading through ncbi. Therefor we have provided the resfinder.py
scriot that uses Blastn instead. Note, this is not not script that is running
on the CGE server. The CGE server is running the perl script using BlastAll
If you want to download the two external tools from the Blast package, BlastAll
and FormatDB, yourself go to
```url
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST
```
and download the version for your OS with the format:
#### Download Blastn and BioPython
```url
blast-version-architecture-OS.tar.gz
http://biopython.org/DIST/docs/install/Installation.html
```
after unzipping the file, add this command to the end of your ~/bash_profile.
```bash
export PATH=$PATH:/path/to/blast-folder/bin
```url
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
```
where path/to/blast-folder is the folder you unzipped.
At last ResFinder has several Perl dependencies. To install them (this requires
CPAN minus as package manager):
#### Install the cgecore module to python3
```bash
make install
```
The scripts are self contained. You just have to copy them to where they should
be used.
Remember to add the program to your system path if you want to be able to
invoke the program without calling the full path.
If you don't do that you have to write the full path to the program when using
it.
## Test the scripts and database
```bash
cd /path/to/test_dir
cp /path/to/resfinder/test.fsa .
perl /path/to/resfinder/resfinder.pl -d /path/to/resfinder/database \
-b /path/to/blast/parent/dir -i test.fsa -a aminoglycoside -k 90.00 -l 0.60
pip3 install cgecore
```
## Usage
The program can be invoked with the -h option to get help and more information
of the service.
You can run resfinder command line using python3
```bash
Usage: perl resfinder.pl [options]
Options:
-h HELP
Prints a message with options and information to the screen
-d DATABASE
The path to where you have located the database folder
-b BLAST
The path to the location of blast-2.2.26 if it is not added
to the users path (see the install guide in 'README.md')
-i INFILE
Your input file which needs to be preassembled partial
or complete genomes in fasta format
-o OUTFOLDER
The folder you want to have your output files places.
If not specified the program will create a folder named
'Output' in which the result files will be stored
-a ANTIMICROBIAL
Antimicrobial configuration. The options can be found
in the file 'ResFinder_Antimicrobial'
-k THRESHOLD
The threshold for % identity for example '95.00' for 95 %
-l MIN_LENGHT
The minimum length of the overlap ex 0.60 for an overlap
of minimum 60 %
```
#### Example of use with the *database* folder is loacted in the current
#### directory and Blast added to the user's path
```perl
perl resfinder.pl -i test.fsa -o OUTFOLDER -a aminoglycoside -k 90.00 \
-l 0.60
```
#### Example of use with the *database* and *blast-2.2.26* folders loacted in
#### other directories
```perl
perl resfinder.pl -d path/to/database -b path/to/blast-2.2.26 -i \
test.fsa -o OUTFOLDER -a aminoglycoside -k 90.00 -l 0.60
# Example of running resfinder
python3 resfinder.py -i test.fsa -o . -p /path/to/resfinder_db \
-b /path/to/blastn -d aminoglycoside -k 90.00 -l 0.60
# The program can be invoked with the -h option
Usage: resfinder.py [-h] [-i INPUTFILE] [-1 FASTQ1] [-2 FASTQ2] [-o OUT_PATH]
[-b BLAST_PATH] [-p DB_PATH] [-k KMA_PATH]
[-q DB_PATH_KMA] [-d DATABASES] [-l MIN_COV]
[-t THRESHOLD]
optional arguments:
-h, --help show this help message and exit
-i INPUTFILE, --inputfile INPUTFILE
Input file
-1 FASTQ1, --fastq1 FASTQ1
Raw read data file 1.
-2 FASTQ2, --fastq2 FASTQ2
Raw read data file 2 (only required if data is paired-
end).
-o OUT_PATH, --outputPath OUT_PATH
Path to blast output
-b BLAST_PATH, --blastPath BLAST_PATH
Path to blast
-p DB_PATH, --databasePath DB_PATH
Path to the databases
-k KMA_PATH, --kmaPath KMA_PATH
Path to KMA
-q DB_PATH_KMA, --databasePathKMA DB_PATH_KMA
Path to the directories containing the KMA indexed
databases. Defaults to the directory 'kma_indexing'
inside the databasePath directory.
-d DATABASES, --databases DATABASES
Databases chosen to search in - if none are specified
all are used
-l MIN_COV, --min_cov MIN_COV
Minimum coverage default 0.6
-t THRESHOLD, --threshold THRESHOLD
Blast threshold for identity
default minimum 0.9
```
## Web-server
### Web-server
A webserver implementing the methods is available at the [CGE
website](http://www.genomicepidemiology.org/) and can be found here:
https://cge.cbs.dtu.dk/services/ResFinder/
## The Latest Version
The latest version can be found at
https://bitbucket.org/genomicepidemiology/resfinder/overview
## Documentation
### Documentation
The documentation available as of the date of this release can be found at
https://bitbucket.org/genomicepidemiology/resfinder/overview.
......
UPDATE_DB deleted 100755 → 0
View file @ a77d84ce
#!/bin/bash
# INPUT: path_to_db
# Check if the user provided the input
if [ -z "$1" ]; then
cwd=$(pwd)
echo "Current path: "$cwd
echo "Type the path to where the database is located, followed by [ENTER]:"
read path
else
path=$1
fi
# Check if the path is valid and existing
if [ -d $path ]; then
cd $path
#git stash
git pull
else
echo "Error: path does not exist! Please provide a valid path..."
fi
echo "Do you want to fix permissions, yes/y or no/n, followed by [ENTER]:"
read fix
if [[ $fix == "yes" ]] || [[ $fix == "y" ]]; then
echo "enter group name followed by [ENTER]:"
read gn
if [ ! -z "$gn" ]; then
chgrp -R $gn $path
fi
find $path \( -name .git \) -prune -printf '' -o -type d -print -exec chmod 775 {} \;
find $path \( -name .git \) -prune -printf '' -o -type f -print -exec chmod 664 {} \;
fi
VALIDATE_DB deleted 100755 → 0
View file @ a77d84ce
#!/usr/bin/env python
''' Validate Database '''
import sys, os
if len(sys.argv) > 1:
db_path = sys.argv[1]
else:
print('Current path: %s'%(os.getcwd()))
db_path = input('Please provide the path to the database:')
# VALIDATE REQUIRED ARGUMENTS
if not os.path.exists(db_path):
sys.exit("Error: The specified database directory does not exist!\n")
else:
# Check existence of config file
db_config_file = '%s/config'%(db_path)
if not os.path.exists(db_config_file):
sys.exit("Error: The database config file could not be found!")
dbs = []
extensions = []
with open(db_config_file) as f:
for l in f:
l = l.strip()
if l == '': continue
if l[0] == '#':
if 'important files are:' in l:
files = ["%s/%s"%(db_path, s.strip())
for s in l.split('are:')[-1].split(',')]
# Check all files exist
for path in files:
if not os.path.exists(path):
sys.exit('Error: %s not found!'%(path))
if 'extensions:' in l:
extensions = [s.strip() for s in l.split('extensions:')[-1].split(',')]
continue
tmp = l.split('\t')
if len(tmp) != 3:
sys.exit(("Error: Invalid line in the database config file!\n"
"A proper entry requires 3 tab separated columns!\n%s")%(l))
db_prefix = tmp[0].strip()
name = tmp[1].split('#')[0]
description = tmp[2]
# Check if all db files are present
for ext in extensions:
path = "%s/%s.%s"%(db_path, db_prefix, ext)
if not os.path.exists(path):
sys.exit(("Error: The database file (%s) could not be found!")%(
path))
dbs.append((name, db_prefix))
if len(dbs) == 0:
sys.exit("Error: No databases were found in the database config file!")
else:
print("Validation passed. Database is valid.")
\ No newline at end of file
brew.sh deleted 100755 → 0
View file @ a77d84ce
#!/bin/env bash
#
PERLBREW='http://install.perlbrew.pl'
BLASTLINUX='ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-linux.tar.gz'
BLASTMAC='ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-universal-macosx.tar.gz'
BLASTFOLDER=blast
# PerlBrew needs to be installed to manage isolated perl environemnts if missing
command -v perlbrew >/dev/null 2>&1 || {
echo 'Installing Perl brew...'
echo "OS type: ${OSTYPE}"
if [[ "$OSTYPE" == 'linux'* ]]; then
wget -O - http://install.perlbrew.pl | bash
else
curl -L ${PERLBREW} | bash
fi
source ~/perl5/perlbrew/etc/bashrc
echo 'source ~/perl5/perlbrew/etc/bashrc' >> ~/.bash_profile
}
perlbrew init
echo 'Upgrading batchperl'
perlbrew install-patchperl
echo "Do you want to install a local perl? [Y]/[N]"
read answer
if [ $answer == 'Y' ]; then
echo 'Installing perl-5.22.0 ...';
#perlbrew install perl-5.22.0
perlbrew --force install perl-5.22.0
perlbrew switch perl-5.22.0
#cd /root/perl5/perlbrew/build/perl-5.22.0/perl-5.22.0
#make intall
else
echo 'Local perl will be used ...';
fi
echo "Do you want to install a cpanmin locally through perlbrew? [Y]/[N]"
read answer
if [ $answer == 'Y' ]; then
echo 'Installing perlbrew install-cpanm...';
perlbrew install-cpanm
else
echo "Do you want to install a cpanmin as sudo[Y]/[N]"
read answer
if [ $answer == 'Y' ]; then
echo 'Installing cpanmin as sudo...';
curl -L https://cpanmin.us | perl - --sudo App::cpanminus
else
echo 'Assuming cpanm is already installed...'
fi
fi
# Installing NCBI Blast tools if missing
command -v blastall >/dev/null 2>&1 || {
echo 'Installing Blast tools...'
echo "OS type: ${OSTYPE}"
if [[ "$OSTYPE" == 'linux'* ]]; then
curl ${BLASTLINUX} -o ${BLASTFOLDER}.tar.gz
else
curl ${BLASTMAC} -o ${BLASTFOLDER}.tar.gz
fi
tar -zxvf ${BLASTFOLDER}.tar.gz
}
debian/changelog
View file @ 48318920
resfinder (2.3.0-1) UNRELEASED; urgency=medium
resfinder (3.1.0-1) UNRELEASED; urgency=medium
* Initial release (Closes: #<bug>)
TODO: Clarify relation between *.pl and *.py
-- Andreas Tille <tille@debian.org> Thu, 07 Jun 2018 21:55:00 +0200
-- Andreas Tille <tille@debian.org> Thu, 18 Oct 2018 16:36:04 +0200
debian/control
View file @ 48318920
......@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 11~)
Standards-Version: 4.1.4
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/resfinder
Vcs-Git: https://salsa.debian.org/med-team/resfinder.git
Homepage: https://bitbucket.org/genomicepidemiology/resfinder
......
debian/install
View file @ 48318920
*_DB /usr/bin
*.py /usr/bin
*.pl /usr/bin
debian/patches/anonymous_cloning_db.patch deleted 100644 → 0
View file @ a77d84ce
Author: Andreas Tille <tille@debian.org>
Last-Update: Mon, 25 Jun 2018 16:11:04 +0200
Description: Enable annonymous cloning of resfinder_db
--- a/INSTALL_DB
+++ b/INSTALL_DB
@@ -11,7 +11,7 @@ fi
# Check if the path is valid and unexisting
if [ ! -d $path ]; then
- git clone git@bitbucket.org:genomicepidemiology/resfinder_db.git $path
+ LC_ALL=C git clone https://bitbucket.org/genomicepidemiology/resfinder_db.git $path
else
echo "Error: path exists! Please provide a valid and unused path..."
fi
debian/patches/series deleted 100644 → 0
View file @ a77d84ce
anonymous_cloning_db.patch
resfinder.pl
View file @ 48318920
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resfinder.py 0 → 100755
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