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MetaPhlAn: Difference between revisions
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→Initialization
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==Initialization== | ==Initialization== | ||
In order to be used correctly, MetaPhlAn needs to download certain databases from a remote server and then compute indices derived from the components of these databases. On those clusters which do not permit Internet access from the compute nodes, these databases will have to be downloaded using a login node using a tool such as wget, | In order to be used correctly, MetaPhlAn needs to download certain databases from a remote server and then compute indices derived from the components of these databases. On those clusters which do not permit Internet access from the compute nodes, these databases will have to be downloaded using a login node using a tool such as wget, | ||
{{Command|prompt=(ENV) [name@server ~]|wget http://cmprod1.cibio.unitn.it/ | {{Command|prompt=(ENV) [name@server ~]|parallel wget ::: http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103.tar http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103_marker_info.txt.bz2 http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103_species.txt.bz2}} | ||
You can then untar the database file and compute the indices using a job, so as not to put an undue computational burden on the shared login node which you are using. A sample script is the following, | You can then untar the database file and compute the indices using a job, so as not to put an undue computational burden on the shared login node which you are using. A sample script is the following, | ||
{{File | {{File | ||
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module load gcc blast samtools bedtools bowtie2 python/3.9 | module load gcc blast samtools bedtools bowtie2 python/3.9 | ||
cd $HOME | cd $HOME | ||
pbunzip2 -p4 | pbunzip2 -p4 mpa_vJan21_CHOCOPhlAnSGB_202103_marker_info.txt.bz2 | ||
source ENV/bin/activate | source ENV/bin/activate | ||
metaphlan --install --index | metaphlan -nproc 4 --install --index mpa_vJan21_CHOCOPhlAnSGB_202103 --bowtie2db $PWD | ||
}} | }} | ||