SMBL 1.4.5

SnakeMake Bioinformatics Library.

In case of any problem, don’t hesitate to contact me on [e-mail].

Short description

SMBL is a library of some useful rules and Python functions which can be used in Snakemake (https://bitbucket.org/johanneskoester/snakemake/) pipelines. It makes possible to automatically install various bioinformatics programs like read mappers, read simulators, conversion tools, etc. It supports also downloading and conversion of some important references in FASTA format (e.g., human genome).

Installation / upgrade

To install SMBL, you need to have Unix-like operating system (e.g., Linux, MacOS) and Python at least 3.3. Installation / upgrade can be performed using the following command.

pip3 install --upgrade smbl

If SnakeMake has not been installed, yet, it will be installed automatically with SMBL.

The current version of SMBL from git can be installed by

pip3 install --upgrade git+git://github.com/karel-brinda/smbl

Requirements

To be able to download and install software automatically, SMBL requires the following programs to be present in you Unix system:

• wget or curl

• gcc 4.7+

• git

• make

Usage

To use SMBL, you have to import the smbl Python package and include a file with all rules using:

import smbl
include: smbl.include()

Then you can use all supported programs or data. When they appear as input of a rule, they will be downloaded or compiled.

All the programs are installed into ~/.smbl/bin/ and all FASTA files into ~/.smbl/fa/.

Programs

Program	Variable with its filename	Link
art_454	smbl.prog.ART_454	http://www.niehs.nih.gov/research/resources/software/biostatistics/art/
art_illumina	smbl.prog.ART_ILLUMINA	http://www.niehs.nih.gov/research/resources/software/biostatistics/art/
art_solid	smbl.prog.ART_SOLID	http://www.niehs.nih.gov/research/resources/software/biostatistics/art/
bcftools	smbl.prog.BCFTOOLS	http://github.com/samtools/bcftools
bfast	smbl.prog.BFAST	http://github.com/nh13/bfast
bgzip	smbl.prog.BGZIP	http://github.com/samtools/htslib
bowtie2	smbl.prog.BOWTIE2	http://github.com/BenLangmead/bowtie2
bowtie2-build	smbl.prog.BOWTIE2_BUILD	http://github.com/BenLangmead/bowtie2
bowtie2-inspect	smbl.prog.BOWTIE2_INSPECT	http://github.com/BenLangmead/bowtie2
bwa	smbl.prog.BWA	http://github.com/lh3/bwa
curesim.jar	smbl.prog.CURESIM	http://www.pegase-biosciences.com/tools/curesim/
curesim_eval.jar	smbl.prog.CURESIM_EVAL	http://www.pegase-biosciences.com/tools/curesim/
deez	smbl.prog.DEEZ	http://github.com/sfu-compbio/deez
drfast	smbl.prog.DRFAST	http://github.com/BilkentCompGen/drfast
dwgsim	smbl.prog.DWGSIM	http://github.com/nh13/dwgsim
dwgsim_eval.pl	smbl.prog.DWGSIM_EVAL	http://github.com/nh13/dwgsim
freec	smbl.prog.FREEC	http://bioinfo-out.curie.fr/projects/freec/
gem-indexer	smbl.prog.GEM_INDEXER	http://algorithms.cnag.cat/wiki/The_GEM_library
gem-mapper	smbl.prog.GEM_MAPPER	http://algorithms.cnag.cat/wiki/The_GEM_library
gem-2-sam	smbl.prog.GEM_2_SAM	http://algorithms.cnag.cat/wiki/The_GEM_library
gnuplot4	smbl.prog.GNUPLOT4	http://www.gnuplot.info/
gnuplot5	smbl.prog.GNUPLOT5	http://www.gnuplot.info/
kallisto	smbl.prog.KALLISTO	https://github.com/pachterlab/kallisto
lastal	smbl.prog.LASTAL	http://last.cbrc.jp/
lastdb	smbl.prog.LASTDB	http://last.cbrc.jp/
mason_frag_sequencing	smbl.prog.MASON_FRAG_SEQUENCING	http://packages.seqan.de/mason2/
mason_genome	smbl.prog.MASON_GENOME	http://packages.seqan.de/mason2/
mason_materializer	smbl.prog.MASON_MATERIALIZER	http://packages.seqan.de/mason2/
mason_methylation	smbl.prog.MASON_METHYLATION	http://packages.seqan.de/mason2/
mason_simulator	smbl.prog.MASON_SIMULATOR	http://packages.seqan.de/mason2/
mason_splicing	smbl.prog.MASON_SPLICING	http://packages.seqan.de/mason2/
mason_variator	smbl.prog.MASON_VARIATOR	http://packages.seqan.de/mason2/
mrfast	smbl.prog.MRFAST	http://github.com/BilkentCompGen/mrfast
mrsfast	smbl.prog.MRSFAST	http://mrsfast.sourceforge.net/
perm	smbl.prog.PERM	http://code.google.com/p/perm/
pbsim	smbl.prog.PBSIM	https://code.google.com/p/pbsim
picard	smbl.prog.PICARD	http://broadinstitute.github.io/picard/
sambamba	smbl.prog.SAMBAMBA	http://lomereiter.github.io/sambamba/
samtools	smbl.prog.SAMTOOLS	http://github.com/samtools/samtools
sirfast	smbl.prog.SIRFAST	http://github.com/BilkentCompGen/sirfast
storm-color	smbl.prog.STORM_COLOR	http://bioinfo.lifl.fr/yass/iedera_solid/storm/
storm-nucleotide	smbl.prog.STORM_NUCLEOTIDE	http://bioinfo.lifl.fr/yass/iedera_solid/storm/
tabix	smbl.prog.TABIX	http://github.com/samtools/htslib
twoBitToFa	smbl.prog.TWOBITTOFA	http://hgdownload.cse.ucsc.edu/admin/exe/
vcfutils.pl	smbl.prog.VCFTULS	http://github.com/samtools/bcftools
wgsim	smbl.prog.WGSIM	http://github.com/lh3/wgsim
wgsim_eval.pl	smbl.prog.WGSIM_EVAL	http://github.com/lh3/wgsim
xs	smbl.prog.XS	http://bioinformatics.ua.pt/software/xs/

FASTA files

FASTA file	Variable with its filename
An example small FASTA file	smbl.fasta.EXAMPLE_1
An example small FASTA file	smbl.fasta.EXAMPLE_2
An example small FASTA file	smbl.fasta.EXAMPLE_3
Human genome HG38 (GRCh38)	smbl.fasta.HG38, smbl.fasta.HUMAN_GRCH38
Mouse genome MM10	smbl.fasta.MOUSE_MM10
Chimpanzee genome PANTR04	smbl.fasta.CHIMP_PANTRO4

Example

The following example demonstrates how SMBL can be used for automatic installation of software.

Create an empty file named Snakefile with the following content:

import smbl
include: smbl.include()

rule all:
        input:
                smbl.prog.DWGSIM,
                smbl.prog.BWA,
                smbl.fasta.EXAMPLE
        params:
                PREF="simulated_reads",
                INDEX="bwa_index"
        output:
                "alignment.sam"
        run:
                # read simulation
                shell("{input[0]} -C 1 {input[2]} {params.PREF}")

                # creating BWA index of the reference sequence
                shell("{input[1]} index {input[2]}")

                # mapping by BWA
                shell("{input[1]} mem {input[2]} {params.PREF}.bfast.fastq > alignment.sam")

Run the script.

snakemake

What happens:

1. An example FASTA file is downloaded

2. DwgSim and BWA are downloaded, compiled and installed

3. DwgSim simulates reads from the example Fasta file

4. These reads are mapped back to the reference by BWA (alignment.sam is created)