How Do I Install and Use Bioperl on Ubuntu 14.04.1 LTS

Bioperl is necessary to run several Perl script which can save your day. Although Perl already comes with Ubuntu but Bioperl should be install manually. I tried to install Bioperl following the instruction given on the official page of Bioperlon my Ubuntu 14.04.1 LTS but it always ends with error. Then I realised that I can directly download the Bioperl from Ubuntu packages by typing a simple command. Even I don't have to go through CPAN. I also share methods th install Bioperl on Windows mechine HERE. Just type this command in your terminal and you are done. So this is the easiest way to install the Bioperl ever
sudo apt-get install bioperl
Simply run this Perl script in your terminal. If it end without any error then you are set.
#!/bin/perl -w
use Bio::Seq;
Finally, How to install a new Perl module? It is also very easy. Just type a simple command in your terminal and done
cpan Bio::Seq
Here Bio::Seq is is the name of Perl module I want to install. You can replace it with whatever Perl module name you want to install.
Note to me
It is not necessary but you may have to add these module to your path
bp_aacomp, bp_biblio, bp_biofetch_genbank_proxy, bp_bioflat_index, bp_biogetseq, bp_blast2tree, bp_bulk_load_gff, bp_chaos_plot, bp_classify_hits_kingdom, bp_composite_LD, bp_das_server, bp_dbsplit, bp_download_query_genbank, bp_einfo, bp_extract_feature_seq, bp_fast_load_gff, bp_fastam9_to_table, bp_fetch, bp_filter_search, bp_flanks, bp_gccalc, bp_genbank2gff, bp_genbank2gff3, bp_generate_histogram, bp_heterogeneity_test, bp_hivq, bp_hmmer_to_table, bp_index, bp_load_gff, bp_local_taxonomydb_query, bp_make_mrna_protein, bp_mask_by_search, bp_meta_gff, bp_mrtrans, bp_mutate, bp_netinstall, bp_nexus2nh, bp_nrdb, bp_oligo_count, bp_pairwise_kaks, bp_parse_hmmsearch, bp_process_gadfly, bp_process_sgd, bp_process_wormbase, bp_query_entrez_taxa, bp_remote_blast, bp_revtrans-motif, bp_search2BSML, bp_search2alnblocks, bp_search2gff, bp_search2table, bp_search2tribe, bp_seq_length, bp_seqconvert, bp_seqfeature_delete, bp_seqfeature_gff3, bp_seqfeature_load, bp_seqret, bp_seqretsplit, bp_split_seq, bp_sreformat, bp_taxid4species, bp_taxonomy2tree, bp_translate_seq, bp_tree2pag, bp_unflatten_seq 

Extract Part of a FASTA Sequences with Position by python script HERE
Update - 1:  If you want to install Bioperl on any instance of Atmosphere of iPlant then log in password of iplant will work as a root password for ubuntu/linux server.

No comments:

Post a Comment

Have Problem ?? Drop a comments here!