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Native Installation
A certain level of Unix command-line computing experience is required to install HBV-GLUE 'natively' (i.e. without using Docker).
A working installation of offline HBV-GLUE is capable of a broad range of analysis functions. A couple are given below;
- Install the GLUE engine
- Download an HBV-GLUE project build
- Install the project build into the GLUE database
- Check that the MAFFT, RAxML and BLAST+ integrations are working correctly
Please post a question on the GLUE support forum with any questions or queries about offline HBV-GLUE
Please follow the native installation instructions on the GLUE website. The BLAST+, MAFFT and RAxML integration steps are required for most uses of Offline HBV-GLUE.
There are two alternative builds for Offline HBV-GLUE. The smaller build includes the minimum set of packages for genotyping. The larger build also includes the NCBI-HBV-GLUE extension, i.e. HBV sequences derived from the NCBI nucleotide database and their metadata.
- HBV-GLUE core project: Download hbv_glue.sql.gz
- HBV-GLUE core project + NCBI-HBV-GLUE extension: Download ncbi_hbv_glue.sql.gz
Warning: This step will overwrite any data currently in the GLUE database.
Unzip the package and load into your MySQL databse using a Unix command line, something like this:
$ gunzip -c ncbi_hbv_glue.sql.gz | /usr/local/mysql/bin/mysql --user=gluetools --password=glue12345 GLUE_TOOLS
Start the GLUE command line and use the list project GLUE command to validate that the project installed.
% gluetools.sh
GLUE version 1.1.66
Mode path: /
GLUE> list project
+======+============================================+
| name | description |
+======+============================================+
| hbv | A GLUE project for Hepatitis B virus (hbv) |
+======+============================================+
Projects found: 1
We will use the hbvMaxLikelihoodGenotyper module within HBV-GLUE to assign a genotype and subgenotype for a sequence in a FASTA file. This will validate that MAFFT and RAxML are integrated and working correctly.
Download the example sequence file and make sure a copy is present inside the directory from which you launched GLUE.
Enter the GLUE commands indicated below and check the output.
GLUE> project hbv
OK
Mode path: /project/hbv
GLUE> module hbvMaxLikelihoodGenotyper genotype file --fileName fullGenome1.fasta
+=============+===================+====================+=======================+
| queryName | speciesFinalClade | genotypeFinalClade | subgenotypeFinalClade |
+=============+===================+====================+=======================+
| fullGenome1 | AL_MASTER | AL_A | AL_A2 |
+=============+===================+====================+=======================+
We will use the hbvFastaSequenceReporter module within HBV-GLUE to translate the RT region of this sequence to amino acids. This step uses BLAST+ to align the sequence with a reference, and so if the step works it validates that BLAST+ is integrated and working correctly.
Enter the GLUE command indicated below and check the output. Use 'Q' to exit the interactive table.
GLUE> module hbvFastaSequenceReporter amino-acid -i fullGenome1.fasta -r REF_NUMBERING_X02763 -f RT -t REF_A2_EU594385 -a AL_UNCONSTRAINED
+=========+============+=========+==========+============+==========+===========+============+============+
| feature | codonLabel | queryNt | relRefNt |dependentNts| codonNts | aminoAcid |definiteAas |possibleAas |
+=========+============+=========+==========+============+==========+===========+============+============+
| RT | 1 | 130 | 130 |GAG | GAG | E |E |E |
| RT | 2 | 133 | 133 |GAC | GAC | D |D |D |
| RT | 3 | 136 | 136 |TGG | TGG | W |W |W |
| RT | 4 | 139 | 139 |GGA | GGA | G |G |G |
| RT | 5 | 142 | 142 |CCC | CCC | P |P |P |
| RT | 6 | 145 | 145 |TGT | TGT | C |C |C |
| RT | 7 | 148 | 148 |GAC | GAC | D |D |D |
| RT | 8 | 151 | 151 |GAA | GAA | E |E |E |
| RT | 9 | 154 | 154 |CAT | CAT | H |H |H |
| RT | 10 | 157 | 157 |GGA | GGA | G |G |G |
| RT | 11 | 160 | 160 |GAA | GAA | E |E |E |
| RT | 12 | 163 | 163 |CAT | CAT | H |H |H |
| RT | 13 | 166 | 166 |CAC | CAC | H |H |H |
| RT | 14 | 169 | 169 |ATC | ATC | I |I |I |
| RT | 15 | 172 | 172 |AGG | AGG | R |R |R |
| RT | 16 | 175 | 175 |ATT | ATT | I |I |I |
| RT | 17 | 178 | 178 |CCT | CCT | P |P |P |
| RT | 18 | 181 | 181 |AGG | AGG | R |R |R |
| RT | 19 | 184 | 184 |ACC | ACC | T |T |T |
| RT | 20 | 187 | 187 |CCT | CCT | P |P |P |
+=========+============+=========+==========+============+==========+===========+============+============+
Rows 1 to 20 of 344 [F:first, L:last, P:prev, N:next, Q:quit]