Re: Biopieces and others questions

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Martin Asser Hansen

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Apr 2, 2016, 3:27:52 AM4/2/16
to Nicolas Lichilin, biop...@googlegroups.com
Hello Nicolas,

YAML is yet-another-markup-language which is typically used for reading and writing configuration files. If you have a Ruby compiled without YAML support, you will get a warning everytime you execute Ruby and that is annoying, but not critical. Biopieces should still work.

I realize that you are trying to run the biopieces installer, which is a leftover from when Biopieces lived at Google Code. Now that Biopieces live at Github we only do the Github checkout.

So lets consolidate. Here is what I have:

Ruby stuff:

maasha@edna:~$ ruby --version
ruby 2.2.3p173 (2015-08-18 revision 51636) [x86_64-darwin14]
maasha@edna:~$ which ruby
/usr/local/bin/ruby
maasha@edna:~$ gem --version
2.4.8
maasha@edna:~$ which gem
/usr/local/bin/gem

Perl stuff:

maasha@edna:~$ perl --version

This is perl 5, version 18, subversion 2 (v5.18.2) built for darwin-thread-multi-2level
(with 2 registered patches, see perl -V for more detail)

Copyright 1987-2013, Larry Wall

Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl".  If you have access to the
Internet, point your browser at http://www.perl.org/, the Perl Home Page.

maasha@edna:~$ which perl
/usr/bin/perl

Bashrc:

maasha@edna:~$ cat .bashrc

PS1='\u@\h:\w\$ ' # Set a fancy prompt

export BP_DIR="/Users/maasha/install/src/biopieces"
export BP_DATA="/Users/maasha/data/BP_DATA"
export BP_TMP="/Users/maasha/scratch/tmp"
export BP_LOG="/Users/maasha/BP_LOG"

source "$BP_DIR/config/bashrc"


And remember that once the ~/.bashrc is written you need to source this, or relogin to give it effect!

You should be able to do this:

maasha@edna:~$ env | grep BP
BP_PERL=/Users/maasha/install/src/biopieces/src/perl
BP_PYTHON=/Users/maasha/install/src/biopieces/src/python
BP_BIN=/Users/maasha/install/src/biopieces/bin
BP_WWW=/Users/maasha/install/src/biopieces/www
BP_DATA=/Users/maasha/data/BP_DATA
BP_TMP=/Users/maasha/scratch/tmp
BP_LOG=/Users/maasha/BP_LOG
BP_DIR=/Users/maasha/install/src/biopieces
BP_C=/Users/maasha/install/src/biopieces/src/c
BP_RUBY=/Users/maasha/install/src/biopieces/src/ruby


So now I can run:

maasha@edna:~$ which read_fasta
/Users/maasha/install/src/biopieces/bin/read_fasta

maasha@edna:~$ read_fasta

Biopiece: read_fasta

Usage

   read_fasta [options] -i <FASTA file(s)>

Options

   [-?          | --help]               #  Print full usage description.
   [-i <files!> | --data_in=<files!>]   #  Comma separated list of files or glob expression to read.
   [-n <uint>   | --num=<uint>]         #  Limit number of records to read.
   [-I <file>   | --stream_in=<file!>]  #  Read input stream from file  -  Default=STDIN
   [-O <file>   | --stream_out=<file>]  #  Write output stream to file  -  Default=STDOUT
   [-v          | --verbose]            #  Verbose output.

Help

read_fasta is part of the Biopieces framework.



And most importantly, I can run bp_test which is an alias (alias bp_test='/Users/maasha/install/src/biopieces/tests/test_all'):


maasha@edna:~$ bp_test
Testing Perl version ... OK
Testing required Perl module - "Inline": OK
Testing required Perl module - "SVG": OK
Testing required Perl module - "Time::HiRes": OK
Testing Ruby version ... OK
Testing required Ruby gem - "gnuplot": OK
Testing required Ruby gem - "narray": OK
Testing required Ruby gem - "RubyInline": OK
Testing required Ruby gem - "terminal-table": OK
Testing auxiliary program - "blastall": OK
Testing auxiliary program - "blat": WARNING
Testing auxiliary program - "bwa": WARNING
Testing auxiliary program - "bowtie": WARNING
Testing auxiliary program - "bowtie2": WARNING
Testing auxiliary program - "formatdb": OK
Testing auxiliary program - "hmmsearch": WARNING
Testing auxiliary program - "gnuplot": OK
Testing auxiliary program - "idba_hybrid": WARNING
Testing auxiliary program - "muscle": OK
Testing auxiliary program - "mummer": OK
Testing auxiliary program - "mysql": WARNING
Testing auxiliary program - "prodigal": OK
Testing auxiliary program - "Ray": OK
Testing auxiliary program - "scan_for_matches": OK
Testing auxiliary program - "usearch": OK
Testing auxiliary program - "velveth": WARNING
Testing auxiliary program - "velvetg": WARNING
Testing auxiliary program - "vmatch": WARNING
Testing add_ident -I $BP_DIR/tests/in/add_ident.in -O $BP_TMP/maasha.add_ident.out ... OK
Testing add_ident -I $BP_DIR/tests/in/add_ident.in -k CUSTOM_KEY -O $BP_TMP/maasha.add_ident.out ... OK
Testing add_ident -I $BP_DIR/tests/in/add_ident.in -p PREFIX -O $BP_TMP/maasha.add_ident.out ... OK
Testing add_ident -I $BP_DIR/tests/in/add_ident.in -o 5 -O $BP_TMP/maasha.add_ident.out ... OK
Testing align_seq -I $BP_DIR/tests/in/align_seq.in -O $BP_TMP/maasha.align_seq.out ... OK
Testing analyze_assembly -I $BP_DIR/tests/in/analyze_assembly.in -O $BP_TMP/maasha.analyze_assembly.out ... OK
Testing analyze_assembly -I $BP_DIR/tests/in/analyze_assembly.in -o $BP_TMP/maasha.analyze_assembly.out -x ... OK
Testing analyze_gc -I $BP_DIR/tests/in/analyze_gc.in -O $BP_TMP/maasha.analyze_gc.out ... OK
Testing analyze_scores -I $BP_DIR/tests/in/analyze_scores.in -O $BP_TMP/maasha.analyze_scores.out ... OK
Testing analyze_seq -I $BP_DIR/tests/in/analyze_seq.in -O $BP_TMP/maasha.analyze_seq.out ... OK
Testing analyze_vals -I $BP_DIR/tests/in/analyze_vals.in -O $BP_TMP/maasha.analyze_vals.out ... OK
Testing analyze_vals -I $BP_DIR/tests/in/analyze_vals.in -O $BP_TMP/maasha.analyze_vals.out -x ... OK
Testing analyze_vals -I $BP_DIR/tests/in/analyze_vals.in -k V0 -O $BP_TMP/maasha.analyze_vals.out ... OK
Testing analyze_vals -I $BP_DIR/tests/in/analyze_vals.in -K V0 -O $BP_TMP/maasha.analyze_vals.out ... OK
Testing analyze_vals -I $BP_DIR/tests/in/analyze_vals.in -o $BP_TMP/maasha.analyze_vals.out -x ... OK
Testing assemble_pairs -I $BP_DIR/tests/in/assemble_pairs.in -O $BP_TMP/maasha.assemble_pairs.out ... OK
Testing assemble_pairs -o 70 -I $BP_DIR/tests/in/assemble_pairs.in -O $BP_TMP/maasha.assemble_pairs.out ... OK
Testing bin_vals -I $BP_DIR/tests/in/bin_vals.in -k V0 -O $BP_TMP/maasha.bin_vals.out ... OK
Testing bin_vals -I $BP_DIR/tests/in/bin_vals.in -k V0 -b 5 -O $BP_TMP/maasha.bin_vals.out ... OK
Testing blast_seq -I $BP_DIR/tests/in/blast_seq.in.2 -d $BP_TMP/maasha.test_tmp/nucleotide -O $BP_TMP/maasha.blast_seq.out ... OK
Testing blast_seq -I $BP_DIR/tests/in/blast_seq.in.2 -d $BP_TMP/maasha.test_tmp/protein -O $BP_TMP/maasha.blast_seq.out ... FAIL
Testing blast_seq -I $BP_DIR/tests/in/blast_seq.in.4 -d $BP_TMP/maasha.test_tmp/nucleotide -O $BP_TMP/maasha.blast_seq.out ... FAIL
Testing blast_seq -I $BP_DIR/tests/in/blast_seq.in.4 -d $BP_TMP/maasha.test_tmp/protein -O $BP_TMP/maasha.blast_seq.out ... FAIL
Testing blast_seq -I $BP_DIR/tests/in/blast_seq.in.2 -d $BP_TMP/maasha.test_tmp/nucleotide -p tblastx -O $BP_TMP/maasha.blast_seq.out ... OK
Testing blast_seq_pair -I $BP_DIR/tests/in/blast_seq_pair.in.1 -O $BP_TMP/maasha.blast_seq_pair.out ... FAIL
Testing blast_seq_pair -I $BP_DIR/tests/in/blast_seq_pair.in.2 -O $BP_TMP/maasha.blast_seq_pair.out ... FAIL
Testing blast_seq_pair -I $BP_DIR/tests/in/blast_seq_pair.in.3 -O $BP_TMP/maasha.blast_seq_pair.out ... FAIL
Testing blast_seq_pair -I $BP_DIR/tests/in/blast_seq_pair.in.4 -O $BP_TMP/maasha.blast_seq_pair.out ... FAIL
Testing blast_seq_pair -I $BP_DIR/tests/in/blast_seq_pair.in.1 -p tblastx -O $BP_TMP/maasha.blast_seq_pair.out ... FAIL
Testing calc_N50 -I $BP_DIR/tests/in/calc_N50.in -O $BP_TMP/maasha.calc_N50.out ... OK
Testing calc_N50 -I $BP_DIR/tests/in/calc_N50.in -o $BP_TMP/maasha.calc_N50.out -x ... OK
Testing calc_bit_scores -I $BP_DIR/tests/in/calc_bit_scores.in -O $BP_TMP/maasha.calc_bit_scores.out ... OK
Testing clip_adaptor -I $BP_DIR/tests/in/clip_adaptor.in -O $BP_TMP/maasha.clip_adaptor.out ... OK
Testing clip_seq -I $BP_DIR/tests/in/clip_seq.in -O $BP_TMP/maasha.clip_seq.out ... OK
Testing complement_seq -I $BP_DIR/tests/in/complement_seq.in -O $BP_TMP/maasha.complement_seq.out ... OK
Testing create_blast_index -I $BP_DIR/tests/in/create_blast_index.in.1 -d $BP_TMP/maasha.test_tmp -i 'index' -x ... OK
Testing create_blast_index -I $BP_DIR/tests/in/create_blast_index.in.2 -d $BP_TMP/maasha.test_tmp -i 'index' -x ... OK
Testing create_seq_index -I $BP_DIR/tests/in/create_seq_index.in -d $BP_TMP/maasha.test_tmp -i test -x ... OK
Testing digest_seq -p GGATCC -c 1 -I $BP_DIR/tests/in/digest_seq.in -O $BP_TMP/maasha.digest_seq.out ... OK
Testing digest_seq -p GGACTT -c 1 -I $BP_DIR/tests/in/digest_seq.in -O $BP_TMP/maasha.digest_seq.out ... OK
Testing digest_seq -p GGATCC -c 1000 -I $BP_DIR/tests/in/digest_seq.in -O $BP_TMP/maasha.digest_seq.out ... OK
Testing digest_seq -p GGATCC -c -1000 -I $BP_DIR/tests/in/digest_seq.in -O $BP_TMP/maasha.digest_seq.out ... OK
Testing duplicate_record -I $BP_DIR/tests/in/duplicate_record.in -k COUNT -O $BP_TMP/maasha.duplicate_record.out ... OK
Testing find_SNPs -I $BP_DIR/tests/in/find_SNPs.in -O $BP_TMP/maasha.find_SNPs.out ... OK
Testing find_SNPs -I $BP_DIR/tests/in/find_SNPs.in -c -O $BP_TMP/maasha.find_SNPs.out ... OK
Testing find_adaptor -m 0 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -I $BP_DIR/tests/in/find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 0 -i 0 -d 0 -F TCGTATGCCGTCTTCTGCTT -I $BP_DIR/tests/in/find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 0 -i 0 -d 0 -r TGACTACGACTACGACTACT -I $BP_DIR/tests/in/find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 0 -i 0 -d 0 -R TGACTACGACTACGACTACT -I $BP_DIR/tests/in/find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 0 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -r TGACTACGACTACGACTACT -I $BP_DIR/tests/in/find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 0 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -l 1 -r TGACTACGACTACGACTACT -I $BP_DIR/tests/in/find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 0 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -l 1 -r TGACTACGACTACGACTACT -L 1 -I $BP_DIR/tests/in/find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 10 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -r TGACTACGACTACGACTACT -I $BP_DIR/tests/in/find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 0 -i 10 -d 0 -f TCGTATGCCGTCTTCTGCTT -r TGACTACGACTACGACTACT -I $BP_DIR/tests/in/find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_adaptor -m 0 -i 0 -d 10 -f TCGTATGCCGTCTTCTGCTT -r TGACTACGACTACGACTACT -I $BP_DIR/tests/in/find_adaptor.in -O $BP_TMP/maasha.find_adaptor.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -r -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -rg -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -rgb $BP_DIR/tests/in/find_barcodes.in.2 -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -r -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -rg -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -rgb $BP_DIR/tests/in/find_barcodes.in.2 -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -m 1 -r -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -m 1 -rg -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -m 1 -rgb $BP_DIR/tests/in/find_barcodes.in.2 -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -m 2 -r -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -m 2 -rg -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -m 2 -rgb $BP_DIR/tests/in/find_barcodes.in.2 -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_barcodes -I $BP_DIR/tests/in/find_barcodes.in.1 -p 4 -m 2 -Rrg -O $BP_TMP/maasha.find_barcodes.out ... OK
Testing find_gaps -I $BP_DIR/tests/in/find_gaps.in -O $BP_TMP/maasha.find_gaps.out ... OK
Testing find_gaps -I $BP_DIR/tests/in/find_gaps.in -m 3 -O $BP_TMP/maasha.find_gaps.out ... OK
Testing find_homopolymers -I $BP_DIR/tests/in/find_homopolymers.in -O $BP_TMP/maasha.find_homopolymers.out ... OK
Testing find_homopolymers -I $BP_DIR/tests/in/find_homopolymers.in -m 3 -O $BP_TMP/maasha.find_homopolymers.out ... OK
Testing find_homopolymers -I $BP_DIR/tests/in/find_homopolymers.in -m 3 -l 1 -O $BP_TMP/maasha.find_homopolymers.out ... OK
Testing find_homopolymers -I $BP_DIR/tests/in/find_homopolymers.in -m 3 -L -O $BP_TMP/maasha.find_homopolymers.out ... OK
Testing find_orfs -I $BP_DIR/tests/in/find_orfs.in -O $BP_TMP/maasha.find_orfs.out ... OK
Testing find_orfs -I $BP_DIR/tests/in/find_orfs.in -s 'GTG' -O $BP_TMP/maasha.find_orfs.out ... OK
Testing find_orfs -I $BP_DIR/tests/in/find_orfs.in -S 'TAA' -O $BP_TMP/maasha.find_orfs.out ... OK
Testing find_orfs -I $BP_DIR/tests/in/find_orfs.in -m 700 -O $BP_TMP/maasha.find_orfs.out ... OK
Testing find_orfs -I $BP_DIR/tests/in/find_orfs.in -M 100 -O $BP_TMP/maasha.find_orfs.out ... OK
Testing find_orfs -I $BP_DIR/tests/in/find_orfs.in -n -O $BP_TMP/maasha.find_orfs.out ... OK
Testing find_orphans -I $BP_DIR/tests/in/find_orphans.in.1 -O $BP_TMP/maasha.find_orphans.out ... OK
Testing find_orphans -I $BP_DIR/tests/in/find_orphans.in.2 -O $BP_TMP/maasha.find_orphans.out ... OK
Testing find_pairs -I $BP_DIR/tests/in/find_pairs.in -O $BP_TMP/maasha.find_pairs.out ... OK
Testing get_seq -i $BP_TMP/maasha.test_tmp/test -s test1 -b 10 -O $BP_TMP/maasha.get_seq.out ... OK
Testing get_seq -i $BP_TMP/maasha.test_tmp/test -s test1 -e 10 -O $BP_TMP/maasha.get_seq.out ... OK
Testing get_seq -i $BP_TMP/maasha.test_tmp/test -s test1 -l 10 -O $BP_TMP/maasha.get_seq.out ... OK
Testing get_seq -i $BP_TMP/maasha.test_tmp/test -s test1 -b 10 -l 10 -O $BP_TMP/maasha.get_seq.out ... OK
Testing get_seq -I $BP_DIR/tests/in/get_seq.in.2 -i $BP_TMP/maasha.test_tmp/test -O $BP_TMP/maasha.get_seq.out ... OK
Testing grab -I $BP_DIR/tests/in/grab.in -p SEQ -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/grab.in -p SEQ,COUNT -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/grab.in -P $BP_DIR/tests/in/grab.in.pat -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/grab.in -p SEQ -i -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/grab.in -p SEQ -K -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/grab.in -p SEQ -V -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/grab.in -p SEQ -k PAT -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/grab.in -r a -k SEQ -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/grab.in -r a -k SEQ -c -O $BP_TMP/maasha.grab.out ... OK
Testing grab -I $BP_DIR/tests/in/grab.in -e 'SEQ_LEN<10' -O $BP_TMP/maasha.grab.out ... OK
Testing index_vals -I $BP_DIR/tests/in/index_vals.in -k MID -O $BP_TMP/maasha.index_vals.out ... OK
Testing join_seq -I $BP_DIR/tests/in/join_seq.in -O $BP_TMP/maasha.join_seq.out ... OK
Testing join_seq -I $BP_DIR/tests/in/join_seq.in -d 'X' -O $BP_TMP/maasha.join_seq.out ... OK
Testing kmer_freq -I $BP_DIR/tests/in/kmer_freq.in -O $BP_TMP/maasha.kmer_freq.out ... OK
Testing length_seq -I $BP_DIR/tests/in/length_seq.in -O $BP_TMP/maasha.length_seq.out ... OK
Testing length_vals -I $BP_DIR/tests/in/length_vals.in -k V0,V1 -O $BP_TMP/maasha.length_vals.out ... OK
Testing lowercase_seq -I $BP_DIR/tests/in/lowercase_seq.in -O $BP_TMP/maasha.lowercase_seq.out ... FAIL
Testing mask_seq -I $BP_DIR/tests/in/mask_seq.in -O $BP_TMP/maasha.mask_seq.out ... OK
Testing mask_seq -I $BP_DIR/tests/in/mask_seq.in -c 0 -O $BP_TMP/maasha.mask_seq.out ... OK
Testing mask_seq -I $BP_DIR/tests/in/mask_seq.in -h -O $BP_TMP/maasha.mask_seq.out ... OK
Testing max_vals -I $BP_DIR/tests/in/max_vals.in -k V1,V2 -o $BP_TMP/maasha.max_vals.out -x ... OK
Testing max_vals -I $BP_DIR/tests/in/max_vals.in -l V3 -O $BP_TMP/maasha.max_vals.out ... OK
Testing mean_scores -I $BP_DIR/tests/in/mean_scores.in -O $BP_TMP/maasha.mean_scores.out ... OK
Testing mean_scores -I $BP_DIR/tests/in/mean_scores.in -l -O $BP_TMP/maasha.mean_scores.out ... OK
Testing mean_scores -I $BP_DIR/tests/in/mean_scores.in -l -w 10 -O $BP_TMP/maasha.mean_scores.out ... OK
Testing mean_vals -I $BP_DIR/tests/in/mean_vals.in -k V1,V2 -o $BP_TMP/maasha.mean_vals.out -x ... OK
Testing mean_vals -I $BP_DIR/tests/in/mean_vals.in -l V3 -O $BP_TMP/maasha.mean_vals.out ... OK
Testing median_vals -I $BP_DIR/tests/in/median_vals.in -k V1,V2 -o $BP_TMP/maasha.median_vals.out -x ... OK
Testing median_vals -I $BP_DIR/tests/in/median_vals.in -l V3 -O $BP_TMP/maasha.median_vals.out ... OK
Testing merge_pair_seq -I $BP_DIR/tests/in/merge_pair_seq.in -O $BP_TMP/maasha.merge_pair_seq.out ... OK
Testing min_vals -I $BP_DIR/tests/in/min_vals.in -k V1,V2 -o $BP_TMP/maasha.min_vals.out -x ... OK
Testing min_vals -I $BP_DIR/tests/in/min_vals.in -l V3 -O $BP_TMP/maasha.min_vals.out ... OK
Testing order_pairs -I $BP_DIR/tests/in/order_pairs.in -O $BP_TMP/maasha.order_pairs.out ... OK
Testing patscan_seq -I $BP_DIR/tests/in/patscan_seq.in.1 -p GACT -O $BP_TMP/maasha.patscan_seq.out ... OK
Testing patscan_seq -I $BP_DIR/tests/in/patscan_seq.in.1 -p GACT -c -O $BP_TMP/maasha.patscan_seq.out ... OK
Testing patscan_seq -I $BP_DIR/tests/in/patscan_seq.in.1 -p GACT -i -O $BP_TMP/maasha.patscan_seq.out ... OK
Testing patscan_seq -I $BP_DIR/tests/in/patscan_seq.in.1 -o -p GG -O $BP_TMP/maasha.patscan_seq.out ... OK
Testing patscan_seq -I $BP_DIR/tests/in/patscan_seq.in.2 -p RARP -O $BP_TMP/maasha.patscan_seq.out ... OK
Testing patscan_seq -I $BP_DIR/tests/in/patscan_seq.in.2 -p RARP -i -O $BP_TMP/maasha.patscan_seq.out ... OK
Testing pcr_seq -f CGATCGAGCT -r AGTCAGTCAT -I $BP_DIR/tests/in/pcr_seq.in -O $BP_TMP/maasha.pcr_seq.out ... OK
Testing pcr_seq -f CGATCGAGCT -r AGTCAGTCAT -m 1 -I $BP_DIR/tests/in/pcr_seq.in -O $BP_TMP/maasha.pcr_seq.out ... OK
Testing pcr_seq -F CGATCGAGCT -r AGTCAGTCAT -I $BP_DIR/tests/in/pcr_seq.in -O $BP_TMP/maasha.pcr_seq.out ... OK
Testing pcr_seq -f CGATCGAGCT -R AGTCAGTCAT -I $BP_DIR/tests/in/pcr_seq.in -O $BP_TMP/maasha.pcr_seq.out ... OK
Testing pcr_seq -F CGATCGAGCT -R AGTCAGTCAT -I $BP_DIR/tests/in/pcr_seq.in -O $BP_TMP/maasha.pcr_seq.out ... OK
Testing plot_distribution -k SEQ_LEN -I $BP_DIR/tests/in/plot_distribution.in -o $BP_TMP/maasha.plot_distribution.out -x ... FAIL
Testing read_454 -i $BP_DIR/tests/in/read_454.in -q $BP_DIR/tests/in/read_454.in.qual -O $BP_TMP/maasha.read_454.out ... OK
Testing read_454 -i $BP_DIR/tests/in/read_454.in.gz -q $BP_DIR/tests/in/read_454.in.qual.gz -O $BP_TMP/maasha.read_454.out ... OK
Testing read_454 -i $BP_DIR/tests/in/read_454.in -q $BP_DIR/tests/in/read_454.in.qual -n 1 -O $BP_TMP/maasha.read_454.out ... OK
Testing read_blast_tab -i $BP_DIR/tests/in/read_blast_tab.in -O $BP_TMP/maasha.read_blast_tab.out ... OK
Testing read_blast_tab -i $BP_DIR/tests/in/read_blast_tab.in -n 1 -O $BP_TMP/maasha.read_blast_tab.out ... OK
Testing read_embl -i $BP_DIR/tests/in/read_embl.in -O $BP_TMP/maasha.read_embl.out ... OK
Testing read_embl -i $BP_DIR/tests/in/read_embl.in.gz -O $BP_TMP/maasha.read_embl.out ... OK
Testing read_embl -i $BP_DIR/tests/in/read_embl.in -k AC -O $BP_TMP/maasha.read_embl.out ... OK
Testing read_embl -i $BP_DIR/tests/in/read_embl.in -k AC -f CDS -O $BP_TMP/maasha.read_embl.out ... OK
Testing read_embl -i $BP_DIR/tests/in/read_embl.in -k AC -f CDS -q translation -O $BP_TMP/maasha.read_embl.out ... OK
Testing read_fasta -i $BP_DIR/tests/in/read_fasta.in -O $BP_TMP/maasha.read_fasta.out ... OK
Testing read_fasta -i $BP_DIR/tests/in/read_fasta.in.gz -O $BP_TMP/maasha.read_fasta.out ... OK
Testing read_fasta -i $BP_DIR/tests/in/read_fasta.in -n 1 -O $BP_TMP/maasha.read_fasta.out ... OK
Testing read_fastq -i $BP_DIR/tests/in/read_fastq.in.1 -O $BP_TMP/maasha.read_fastq.out ... OK
Testing read_fastq -i $BP_DIR/tests/in/read_fastq.in.1 -e base_33 -O $BP_TMP/maasha.read_fastq.out ... OK
Testing read_fastq -i $BP_DIR/tests/in/read_fastq.in.2 -O $BP_TMP/maasha.read_fastq.out ... OK
Testing read_fastq -i $BP_DIR/tests/in/read_fastq.in.2 -e base_64 -O $BP_TMP/maasha.read_fastq.out ... OK
Testing read_fastq -i $BP_DIR/tests/in/read_fastq.in.1.gz -O $BP_TMP/maasha.read_fastq.out ... OK
Testing read_fastq -i $BP_DIR/tests/in/read_fastq.in.1 -n 1 -O $BP_TMP/maasha.read_fastq.out ... OK
Testing read_fastq -i $BP_DIR/tests/in/read_fastq.in.3 -j $BP_DIR/tests/in/read_fastq.in.4 -O $BP_TMP/maasha.read_fastq.out ... OK
Testing read_genbank -i $BP_DIR/tests/in/read_genbank.in -O $BP_TMP/maasha.read_genbank.out ... OK
Testing read_genbank -i $BP_DIR/tests/in/read_genbank.in.gz -O $BP_TMP/maasha.read_genbank.out ... OK
Testing read_genbank -i $BP_DIR/tests/in/read_genbank.in -k AC -O $BP_TMP/maasha.read_genbank.out ... OK
Testing read_genbank -i $BP_DIR/tests/in/read_genbank.in -k AC -f CDS -O $BP_TMP/maasha.read_genbank.out ... OK
Testing read_genbank -i $BP_DIR/tests/in/read_genbank.in -k AC -f CDS -q translation -O $BP_TMP/maasha.read_genbank.out ... OK
Testing read_pdb -i $BP_DIR/tests/in/read_pdb.in -o $BP_TMP/maasha.read_pdb.out ... OK
Testing read_pdb -i $BP_DIR/tests/in/read_pdb.in -O $BP_TMP/maasha.read_pdb.out --method=atom -M ... OK
Testing read_pdb -i $BP_DIR/tests/in/read_pdb.in -o $BP_TMP/maasha.read_pdb.out -m seqres -c atom -a CA -r ILE,SER ... OK
Testing read_sff -i $BP_DIR/tests/in/read_sff.in -O $BP_TMP/maasha.read_sff.out ... OK
Testing read_sff -i $BP_DIR/tests/in/read_sff.in -n 1 -O $BP_TMP/maasha.read_sff.out ... OK
Testing read_sff -i $BP_DIR/tests/in/read_sff.in -n 1 -m -O $BP_TMP/maasha.read_sff.out ... OK
Testing read_sff -i $BP_DIR/tests/in/read_sff.in -n 1 -c -O $BP_TMP/maasha.read_sff.out ... OK
Testing read_tab -i $BP_DIR/tests/in/read_tab.in.1 -O $BP_TMP/maasha.read_tab.out ... OK
Testing read_tab -i $BP_DIR/tests/in/read_tab.in.1 -s 1 -O $BP_TMP/maasha.read_tab.out ... OK
Testing read_tab -i $BP_DIR/tests/in/read_tab.in.1 -s 1 -k ORGANISM,SEQ,COUNT -O $BP_TMP/maasha.read_tab.out ... OK
Testing read_tab -i $BP_DIR/tests/in/read_tab.in.1 -s 1 -c 2,1 -O $BP_TMP/maasha.read_tab.out ... OK
Testing read_tab -i $BP_DIR/tests/in/read_tab.in.1 -s 1 -c 2,1 -k COUNT,SEQ -O $BP_TMP/maasha.read_tab.out ... OK
Testing read_tab -i $BP_DIR/tests/in/read_tab.in.2 -O $BP_TMP/maasha.read_tab.out ... OK
Testing read_tab -i $BP_DIR/tests/in/read_tab.in.2 -n 1 -O $BP_TMP/maasha.read_tab.out ... OK
Testing read_tab -i $BP_DIR/tests/in/read_tab.in.3 -d ';' -O $BP_TMP/maasha.read_tab.out ... OK
Testing remove_indel_columns -I $BP_DIR/tests/in/remove_indel_columns.in -O $BP_TMP/maasha.remove_indel_columns.out ... OK
Testing remove_indels -I $BP_DIR/tests/in/remove_indels.in -O $BP_TMP/maasha.remove_indels.out ... OK
Testing remove_keys -I $BP_DIR/tests/in/remove_keys.in -k SEQ_NAME,SEQ -O $BP_TMP/maasha.remove_keys.out ... OK
Testing remove_primers -f ACTGAGCTAGCAGCGGTGCG -r TGCTGGACTGGGTGGAGCAC -m 0 -i 0 -d 0 -I $BP_DIR/tests/in/remove_primers.in -O $BP_TMP/maasha.remove_primers.out ... OK
Testing rename_keys -I $BP_DIR/tests/in/rename_keys.in -k SEQ,FOO -O $BP_TMP/maasha.rename_keys.out ... OK
Testing replace_vals -I $BP_DIR/tests/in/replace_vals.in.1 -k SEQ_NAME -s test1 -r foo -O $BP_TMP/maasha.replace_vals.out ... OK
Testing replace_vals -I $BP_DIR/tests/in/replace_vals.in.1 -k SEQ_NAME -f $BP_DIR/tests/in/replace_vals.in.2 -O $BP_TMP/maasha.replace_vals.out ... OK
Testing replace_vals -I $BP_DIR/tests/in/replace_vals.in.1 -k SEQ_NAME -f $BP_DIR/tests/in/replace_vals.in.2 -S 2 -R 1 -O $BP_TMP/maasha.replace_vals.out ... OK
Testing reverse_seq -I $BP_DIR/tests/in/reverse_seq.in -O $BP_TMP/maasha.reverse_seq.out ... OK
Testing scores_to_dec -I $BP_DIR/tests/in/scores_to_dec.in -O $BP_TMP/maasha.scores_to_dec.out ... OK
Testing shred_seq -I $BP_DIR/tests/in/shred_seq.in -s 18 -c 2 -O $BP_TMP/maasha.shred_seq.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -b 5 -e 10 -O $BP_TMP/maasha.slice_align.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -f TGGCGGCATG -r GCGAACGGGT -m 0 -i 0 -d 0 -O $BP_TMP/maasha.slice_align.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -F CATGCCGCCA -r GCGAACGGGT -m 0 -i 0 -d 0 -O $BP_TMP/maasha.slice_align.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -f TGGCGGCATG -R ACCCGTTCGC -m 0 -i 0 -d 0 -O $BP_TMP/maasha.slice_align.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -f TGGgGGCATG -r GCGAtCGGGT -m 1 -i 0 -d 0 -O $BP_TMP/maasha.slice_align.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -f TGGCGcGCATG -r GCGAtACGGGT -m 0 -i 1 -d 0 -O $BP_TMP/maasha.slice_align.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -f TGGCGCATG -r GCGAAGGGT -m 0 -i 0 -d 1 -O $BP_TMP/maasha.slice_align.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -f ATACGCTGCGGAGGCTA -r TTGCTACCAGGCGTCGAGCGGCGGACGGG -t $BP_DIR/tests/in/slice_align.in.2 -m 0 -d 0 -i 0 -O $BP_TMP/maasha.slice_align.out ... OK
Testing slice_align -I $BP_DIR/tests/in/slice_align.in.1 -b 5 -e 10 -t $BP_DIR/tests/in/slice_align.in.2 -O $BP_TMP/maasha.slice_align.out ... OK
Testing sort_records -I $BP_DIR/tests/in/sort_records.in -k SEQ_LEN -O $BP_TMP/maasha.sort_records.out ... OK
Testing sort_records -I $BP_DIR/tests/in/sort_records.in -k SEQ_LENn -O $BP_TMP/maasha.sort_records.out ... OK
Testing sort_records -I $BP_DIR/tests/in/sort_records.in -k SEQ_LEN -r -O $BP_TMP/maasha.sort_records.out ... OK
Testing split_pair_seq -I $BP_DIR/tests/in/split_pair_seq.in -O $BP_TMP/maasha.split_pair_seq.out ... OK
Testing substitute_vals -I $BP_DIR/tests/in/substitute_vals.in -s '\d' -r '' -O $BP_TMP/maasha.substitute_vals.out ... OK
Testing substitute_vals -I $BP_DIR/tests/in/substitute_vals.in -k SEQ -s 'n' -r '' -O $BP_TMP/maasha.substitute_vals.out ... OK
Testing substitute_vals -I $BP_DIR/tests/in/substitute_vals.in -k SEQ -s 'n' -r '' -i -O $BP_TMP/maasha.substitute_vals.out ... OK
Testing substitute_vals -I $BP_DIR/tests/in/substitute_vals.in -k SEQ -s 'n' -r '' -i -g -O $BP_TMP/maasha.substitute_vals.out ... OK
Testing substitute_vals -I $BP_DIR/tests/in/substitute_vals.in -k SEQ -s 'n{3,}' -r '' -i -g -O $BP_TMP/maasha.substitute_vals.out ... OK
Testing sum_vals -I $BP_DIR/tests/in/sum_vals.in -k V1,V2 -o $BP_TMP/maasha.sum_vals.out -x ... OK
Testing sum_vals -I $BP_DIR/tests/in/sum_vals.in -l V3 -O $BP_TMP/maasha.sum_vals.out ... OK
Testing swapcase_seq -I $BP_DIR/tests/in/swapcase_seq.in -O $BP_TMP/maasha.swapcase_seq.out ... OK
Testing translate_seq -I $BP_DIR/tests/in/translate_seq.in -O $BP_TMP/maasha.translate_seq.out ... OK
Testing translate_seq -I $BP_DIR/tests/in/translate_seq.in -f '1,-1' -O $BP_TMP/maasha.translate_seq.out ... OK
Testing transliterate_seq -I $BP_DIR/tests/in/transliterate_seq.in -s 'N' -r 'A' -O $BP_TMP/maasha.transliterate_seq.out ... OK
Testing transliterate_seq -I $BP_DIR/tests/in/transliterate_seq.in -d 'N' -O $BP_TMP/maasha.transliterate_seq.out ... OK
Testing transliterate_vals -I $BP_DIR/tests/in/transliterate_vals.in -k SEQ -s A -r n -O $BP_TMP/maasha.transliterate_vals.out ... OK
Testing transliterate_vals -I $BP_DIR/tests/in/transliterate_vals.in -k SEQ_NAME -d Tt -O $BP_TMP/maasha.transliterate_vals.out ... OK
Testing trim_seq -I $BP_DIR/tests/in/trim_seq.in -O $BP_TMP/maasha.trim_seq.out ... OK
Testing trim_seq -I $BP_DIR/tests/in/trim_seq.in -m 25 -O $BP_TMP/maasha.trim_seq.out ... OK
Testing trim_seq -I $BP_DIR/tests/in/trim_seq.in -t both -O $BP_TMP/maasha.trim_seq.out ... OK
Testing trim_seq -I $BP_DIR/tests/in/trim_seq.in -t left -O $BP_TMP/maasha.trim_seq.out ... OK
Testing trim_seq -I $BP_DIR/tests/in/trim_seq.in -t right -O $BP_TMP/maasha.trim_seq.out ... OK
Testing trim_seq -I $BP_DIR/tests/in/trim_seq.in -l 4 -O $BP_TMP/maasha.trim_seq.out ... OK
Testing uclust_seq -I $BP_DIR/tests/in/uclust_seq.in -O $BP_TMP/maasha.uclust_seq.out ... OK
Testing uclust_seq -I $BP_DIR/tests/in/uclust_seq.in -C 2 -O $BP_TMP/maasha.uclust_seq.out ... OK
Testing uclust_seq -I $BP_DIR/tests/in/uclust_seq.in -i 1 -O $BP_TMP/maasha.uclust_seq.out ... OK
Testing uclust_seq -I $BP_DIR/tests/in/uclust_seq.in -i 1 -c -O $BP_TMP/maasha.uclust_seq.out ... OK
Testing uniq_seq -I $BP_DIR/tests/in/uniq_seq.in | sort_records -k SEQ -O $BP_TMP/maasha.uniq_seq.out ... OK
Testing uniq_seq -I $BP_DIR/tests/in/uniq_seq.in -c | sort_records -k SEQ -O $BP_TMP/maasha.uniq_seq.out ... OK
Testing uniq_vals -I $BP_DIR/tests/in/uniq_vals.in -k SEQ -O $BP_TMP/maasha.uniq_vals.out ... OK
Testing uniq_vals -I $BP_DIR/tests/in/uniq_vals.in -k SEQ -i -O $BP_TMP/maasha.uniq_vals.out ... OK
Testing uppercase_seq -I $BP_DIR/tests/in/uppercase_seq.in -O $BP_TMP/maasha.uppercase_seq.out ... OK
Testing usearch_seq -I $BP_DIR/tests/in/usearch_seq.in -d $BP_DIR/tests/in/usearch_seq.in.db -i 1 -O $BP_TMP/maasha.usearch_seq.out ... OK
Testing usearch_seq -I $BP_DIR/tests/in/usearch_seq.in -d $BP_DIR/tests/in/usearch_seq.in.db -i 1 -p local -O $BP_TMP/maasha.usearch_seq.out ... FAIL
Testing usearch_seq -I $BP_DIR/tests/in/usearch_seq.in -d $BP_DIR/tests/in/usearch_seq.in.db -i 0.99 -e 0.1 -p local -O $BP_TMP/maasha.usearch_seq.out ... FAIL
Testing usearch_seq -I $BP_DIR/tests/in/usearch_seq.in -d $BP_DIR/tests/in/usearch_seq.in.db -i 0.99 -O $BP_TMP/maasha.usearch_seq.out ... OK
Testing usearch_seq -I $BP_DIR/tests/in/usearch_seq.in -d $BP_DIR/tests/in/usearch_seq.in.db -i 1 -m 1 -O $BP_TMP/maasha.usearch_seq.out ... OK
Testing write_blast -I $BP_DIR/tests/in/write_blast.in -o $BP_TMP/maasha.write_blast.out -x ... OK
Testing write_blast -I $BP_DIR/tests/in/write_blast.in -c -o $BP_TMP/maasha.write_blast.out -x ... OK
Testing write_blast -I $BP_DIR/tests/in/write_blast.in -Z -o $BP_TMP/maasha.write_blast.out.gz -x ... OK
Testing write_fasta -I $BP_DIR/tests/in/write_fasta.in -o $BP_TMP/maasha.write_fasta.out -x ... OK
Testing write_fasta -I $BP_DIR/tests/in/write_fasta.in -w 4 -o $BP_TMP/maasha.write_fasta.out -x ... OK
Testing write_fasta -I $BP_DIR/tests/in/write_fasta.in -w 4 -Z gzip -o $BP_TMP/maasha.write_fasta.out.gz -x ... OK
Testing write_fasta -I $BP_DIR/tests/in/write_fasta.in -w 4 -Z bzip2 -o $BP_TMP/maasha.write_fasta.out.bz2 -x ... OK
Testing write_fasta_files -I $BP_DIR/tests/in/write_fasta_files.in -d $BP_TMP/maasha.test_tmp -k SEQ_NAME -x ... OK
Testing write_fasta_files -I $BP_DIR/tests/in/write_fasta_files.in -d $BP_TMP/maasha.test_tmp -k SEQ_LEN -x ... OK
Testing write_fasta_files -I $BP_DIR/tests/in/write_fasta_files.in -d $BP_TMP/maasha.test_tmp -k SEQ_LEN -Z gzip -x ... OK
Testing write_fasta_files -I $BP_DIR/tests/in/write_fasta_files.in -d $BP_TMP/maasha.test_tmp -k SEQ_LEN -Z bzip2 -x ... OK
Testing write_fasta_files -I $BP_DIR/tests/in/write_fasta_files.in -d $BP_TMP/maasha.test_tmp -k SEQ_LEN -w 4 -x ... OK
Testing write_fasta_files -I $BP_DIR/tests/in/write_fasta_files.in -d $BP_TMP/maasha.test_tmp -k SEQ_NAME -p Length -x ... OK
Testing write_fastq -I $BP_DIR/tests/in/write_fastq.in -o $BP_TMP/maasha.write_fastq.out -x ... OK
Testing write_fastq -I $BP_DIR/tests/in/write_fastq.in -e base_33 -o $BP_TMP/maasha.write_fastq.out -x ... OK
Testing write_fastq -I $BP_DIR/tests/in/write_fastq.in -e base_64 -o $BP_TMP/maasha.write_fastq.out -x ... OK
Testing write_fastq -I $BP_DIR/tests/in/write_fastq.in -Z gzip -o $BP_TMP/maasha.write_fastq.out.gz -x ... OK
Testing write_fastq -I $BP_DIR/tests/in/write_fastq.in -Z bzip2 -o $BP_TMP/maasha.write_fastq.out.bz2 -x ... OK
Testing write_fastq_files -I $BP_DIR/tests/in/write_fastq_files.in -d $BP_TMP/maasha.test_tmp -k SEQ_NAME -x ... OK
Testing write_fastq_files -I $BP_DIR/tests/in/write_fastq_files.in -e base_33 -d $BP_TMP/maasha.test_tmp -k SEQ_NAME -x ... OK
Testing write_fastq_files -I $BP_DIR/tests/in/write_fastq_files.in -e base_64 -d $BP_TMP/maasha.test_tmp -k SEQ_NAME -x ... OK
Testing write_fastq_files -I $BP_DIR/tests/in/write_fastq_files.in -e base_64 -d $BP_TMP/maasha.test_tmp -k SEQ_NAME -Z gzip -x ... OK
Testing write_fastq_files -I $BP_DIR/tests/in/write_fastq_files.in -e base_64 -d $BP_TMP/maasha.test_tmp -k SEQ_NAME -Z bzip2 -x ... OK
Testing write_fastq_files -I $BP_DIR/tests/in/write_fastq_files.in -d $BP_TMP/maasha.test_tmp -k SEQ_NAME -p Name -x ... OK
Testing write_tab -I $BP_DIR/tests/in/write_tab.in -o $BP_TMP/maasha.write_tab.out -x ... OK
Testing write_tab -I $BP_DIR/tests/in/write_tab.in -c -o $BP_TMP/maasha.write_tab.out -x ... OK
Testing write_tab -I $BP_DIR/tests/in/write_tab.in -d ',' -o $BP_TMP/maasha.write_tab.out -x ... OK
Testing write_tab -I $BP_DIR/tests/in/write_tab.in -Z gzip -o $BP_TMP/maasha.write_tab.out.gz -x ... OK
Testing write_tab -I $BP_DIR/tests/in/write_tab.in -Z bzip2 -o $BP_TMP/maasha.write_tab.out.bz2 -x ... OK
Testing write_tab -I $BP_DIR/tests/in/write_tab.in -k 'Count' -o $BP_TMP/maasha.write_tab.out -x ... OK
Testing write_tab -I $BP_DIR/tests/in/write_tab.in -K 'Count' -o $BP_TMP/maasha.write_tab.out -x ... OK
Testing write_tab -I $BP_DIR/tests/in/write_tab.in -p -o $BP_TMP/maasha.write_tab.out -x ... OK
Testing write_tab -I $BP_DIR/tests/in/write_tab.in -p -C -o $BP_TMP/maasha.write_tab.out -x ... OK
Testing write_tab -I $BP_DIR/tests/in/write_tab.in -p -c -C -o $BP_TMP/maasha.write_tab.out -x ... OK
Biopieces tested: 86  Tests run: 293  OK: 271  FAIL: 12  WARNING: 10  Time: 41 secs


I realize, I have some FAILs, but that is me having wrong versions of aux programs - that always change output format for every new release (grrrrrrr). But otherwise everything else is working.


Cheers,


Martin

On Fri, Apr 1, 2016 at 11:08 PM, Nicolas Lichilin <nlic...@yahoo.com> wrote:
Hi Martin, 

Thanks for your soon reply, and your willing  to help me.

Attached are the log files for each step as is detailed in the web page....

I saw some problems as YALM not installed... But I don't know what is this... 
And also: "I cannot determine if you have a C compiler" But i have gcc
>Nicolass-MacBook-Pro:~ nicolaslichilin$ gcc --version
gcc (Homebrew gcc 5.3.0 --without-multilib) 5.3.0


Ok, thanks again for your help.

Bye, 

Nicolas

 


El Viernes, 1 de abril, 2016 20:23:12, Martin Asser Hansen <martin...@gmail.com> escribió:


Hello Nicolas,


Unfortunately, Biopieces installation can be rather frustrating for newcomers. Biopieces cannot be installed with the gem or homebrew commands; you really need to follow the install instructions step-by-step and do record the output for each step and send me.

The Biopieces digest_seq is rather good.


Cheers,


Martin

On Fri, Apr 1, 2016 at 7:13 PM, Nicolas Lichilin <nlic...@yahoo.com> wrote:
Dear Martin,

My name is Nicolas Lichilín. Currently, I'm doing my master thesis related with comparative genomics. Looking for a tool that allows me to do in silico restriction of a full genome and have the sequences file digested, I found Biopieces.

However, It seems that I have some troubles to install it. I have a mac with the latest version 10.11, el capitan. 

I have followed all the instructions in the web site without getting any result. Also, I have tried to install it using Homebrew but there is a problem with the code:

>gem install biopieces
RROR:  Could not find a valid gem 'biopieces' (>= 0) in any repository
ERROR:  Possible alternatives: bio-plates, bits-n-pieces, pieces, time_pieces 

And also I have typed the code:

>bp_test
-bash: bp_test: command not found

But, the command is not found....


Could you help me to install Biopieces? And/or if you could recommend me a software to do the in silico enzyme digestion o the genome? But, having the sequences file as an output. Because, i already used EMBOSS "resctric" command but this is not the output that I'm looking for.

Thanks ins advance.

Kind regards,

Nicolas



 
Nicolás Lichilín Ortiz




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