1. Whats included in this installer ?
This installer includes addition/update of the following tools and hundreds of their dependencies;
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PathoScope2 - Species identification and strain attribution with unassembled sequencing data
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Prokka - Rapid prokaryotic genome annotation
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Roary - Rapid large-scale prokaryote pan genome analysis
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Snippy - Rapid bacterial SNP calling and core genome alignments
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MLST - Scan contig files against PubMLST typing schemes
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Abricate - Mass screening of contigs for antimicrobial and virulence genes
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Sixess - Rapid 16s rRNA identification from isolate FASTQ files
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SalmID - Rapid confirmation of Salmonella spp. and subspp. from sequence data
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MEGAN6 - a comprehensive toolbox for interactively analyzing microbiome data
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MetaPhlAn2 - profiling the composition of microbial communities from metagenomic sequencing data
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QIIME2 - a next-generation microbiome bioinformatics platform
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mothur - software to fill the bioinformatics needs of the microbial ecology community
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Krona Tools - Interactively explore metagenomes
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Staphopia-ap Staphopia analysis pipeline
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MASH - fast genome and metagenome distance estimation using MinHash
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QuickTree - reconstruction of phylogenies for very large protein families
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MashTree - Create a tree using Mash distances
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Wgsim - a small tool for simulating sequence reads from a reference genome
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DAHAK - integrates state-of-the-art open source tools for metagenomic analyses
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vt - a variant tool set that discovers short variants from Next Generation Sequencing data
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MiniMap2 - A versatile pairwise aligner for genomic and spliced nucleotide sequences
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SNP-site - Rapidly extracts SNPs from a multi-FASTA alignment
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NGS tools - methods for population genetics analyses from NGS data
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SamTools 1.8 - a suite of programs for interacting with high-throughput sequencing data
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BcfTools 1.8 - a set of utilities that manipulate variant calls
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Trimmomatic 0.38 - A flexible read trimming tool for Illumina NGS data
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tbl2asn - automates the creation of sequence records for submission to GenBank
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edirect - access to the NCBI’s suite of interconnected databases
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Docker - open platform to build, ship, and run distributed applications
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Conda - Package, dependency and environment management for any language
2. Download Installer
Download the package installer from this link https://molbiocloud.com/help/tiki-download_file.php?fileId=140
3. Prepare for install
3.1. Open a terminal. Move the ‘asm’ installer from your Dowonloads folder to your home folder using the below command (example screenshot below);
(You can also copy/paste the ‘asm’ installer from Downloads folder to the ‘ubuntu’ home folder, using the Desktop GUI interface, like you will do in a PC or MAC.
cp ~/Downloads/asm .
3.2. Make ‘asm’ installer executable, using the below command (example screenshot below)
chmod 755 asm
4. How to run the installer?
Run the script with the following command as example, in your working directory (example screenshot below).
ENTER THE DEFAULT parameters and ‘yes’ for any prompts in the middle of the install. The install should take about 10 minutes.
sudo ./asm
The setup assumes that you have not made any system level changes. If the install does not behave as expected, probably the system configuration has been changed. If you face any issues after this update, please let us know ASAP, so that we can help you troubleshoot the issue.
5. Issues ?
If you have any issues with running the installer or need any other information regarding this, please do not hesitate to contact us at contact at molbiocloud.com