[med-svn] r22630 - in trunk/packages/metaphlan2/trunk/debian: . bin patches
Andreas Tille
tille at moszumanska.debian.org
Mon Jul 25 14:40:22 UTC 2016
Author: tille
Date: 2016-07-25 14:40:21 +0000 (Mon, 25 Jul 2016)
New Revision: 22630
Added:
trunk/packages/metaphlan2/trunk/debian/bin/
trunk/packages/metaphlan2/trunk/debian/bin/metaphlan2_strainer
trunk/packages/metaphlan2/trunk/debian/clean
trunk/packages/metaphlan2/trunk/debian/docs
trunk/packages/metaphlan2/trunk/debian/install
trunk/packages/metaphlan2/trunk/debian/links
trunk/packages/metaphlan2/trunk/debian/manpages
trunk/packages/metaphlan2/trunk/debian/metaphlan2.1
trunk/packages/metaphlan2/trunk/debian/metaphlan2_strainer.1
trunk/packages/metaphlan2/trunk/debian/patches/
trunk/packages/metaphlan2/trunk/debian/patches/fix_sequence.patch
trunk/packages/metaphlan2/trunk/debian/patches/mpa_dir-is-usr_share_metaphlan2.patch
trunk/packages/metaphlan2/trunk/debian/patches/series
Modified:
trunk/packages/metaphlan2/trunk/debian/control
trunk/packages/metaphlan2/trunk/debian/rules
Log:
Some more serious packaging possibly read for testing now
Added: trunk/packages/metaphlan2/trunk/debian/bin/metaphlan2_strainer
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/bin/metaphlan2_strainer (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/bin/metaphlan2_strainer 2016-07-25 14:40:21 UTC (rev 22630)
@@ -0,0 +1,7 @@
+#!/bin/sh
+
+export PYTHONPATH="$PATH:/usr/share/metaphlan2/strainer_src"
+
+cmd=`basename "$0" .py`.py
+
+exec "/usr/share/metaphlan2/$cmd" "$@"
Property changes on: trunk/packages/metaphlan2/trunk/debian/bin/metaphlan2_strainer
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/metaphlan2/trunk/debian/clean
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/clean (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/clean 2016-07-25 14:40:21 UTC (rev 22630)
@@ -0,0 +1 @@
+README.html
Modified: trunk/packages/metaphlan2/trunk/debian/control
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/control 2016-07-25 12:47:08 UTC (rev 22629)
+++ trunk/packages/metaphlan2/trunk/debian/control 2016-07-25 14:40:21 UTC (rev 22630)
@@ -5,7 +5,9 @@
Priority: optional
Build-Depends: debhelper (>= 9),
python-all,
- dh-python
+ dh-python,
+ python-markdown,
+ bowtie2
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/metaphlan2/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/metaphlan2/trunk/
@@ -14,7 +16,11 @@
Package: metaphlan2
Architecture: all
Depends: ${python:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ python-biom-format,
+ python-msgpack,
+ python-pandas,
+ bowtie2
Description: Metagenomic Phylogenetic Analysis
MetaPhlAn is a computational tool for profiling the composition of
microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from
Added: trunk/packages/metaphlan2/trunk/debian/docs
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/docs (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/docs 2016-07-25 14:40:21 UTC (rev 22630)
@@ -0,0 +1 @@
+README.html
Added: trunk/packages/metaphlan2/trunk/debian/install
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/install (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/install 2016-07-25 14:40:21 UTC (rev 22630)
@@ -0,0 +1,5 @@
+*.py usr/share/metaphlan2
+strainer_* usr/share/metaphlan2
+utils usr/share/metaphlan2
+debian/bin usr
+db_v20 usr/share/metaphlan2
Added: trunk/packages/metaphlan2/trunk/debian/links
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/links (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/links 2016-07-25 14:40:21 UTC (rev 22630)
@@ -0,0 +1,2 @@
+usr/share/metaphlan2/metaphlan2.py usr/bin/metaphlan2
+
Added: trunk/packages/metaphlan2/trunk/debian/manpages
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/manpages (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/manpages 2016-07-25 14:40:21 UTC (rev 22630)
@@ -0,0 +1 @@
+debian/*.1
Added: trunk/packages/metaphlan2/trunk/debian/metaphlan2.1
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/metaphlan2.1 (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/metaphlan2.1 2016-07-25 14:40:21 UTC (rev 22630)
@@ -0,0 +1,313 @@
+.TH METAPHLAN2 "1" "July 2016" "metaphlan2 2.5.0" "User Commands"
+.SH NAME
+metaphlan2 \- METAgenomic PHyLogenetic ANalysis for metagenomic taxonomic profiling
+.SH SYNOPSIS
+.B metaphlan2
+ \fB\-\-input_type\fR
+{fastq,fasta,multifasta,multifastq,bowtie2out,sam}
+[\-\-mpa_pkl MPA_PKL] [\-\-bowtie2db METAPHLAN_BOWTIE2_DB]
+[\-\-bt2_ps BowTie2 presets] [\-\-bowtie2_exe BOWTIE2_EXE]
+[\-\-bowtie2out FILE_NAME] [\-\-no_map] [\-\-tmp_dir]
+[\-\-tax_lev TAXONOMIC_LEVEL] [\-\-min_cu_len]
+[\-\-min_alignment_len] [\-\-ignore_viruses]
+[\-\-ignore_eukaryotes] [\-\-ignore_bacteria] [\-\-ignore_archaea]
+[\-\-stat_q] [\-\-ignore_markers IGNORE_MARKERS] [\-\-avoid_disqm]
+[\-\-stat] [\-t ANALYSIS TYPE] [\-\-nreads NUMBER_OF_READS]
+[\-\-pres_th PRESENCE_THRESHOLD] [\-\-clade] [\-\-min_ab] [\-h]
+[\-o output file] [\-\-sample_id_key name] [\-\-sample_id value]
+[\-s sam_output_file] [\-\-biom biom_output] [\-\-mdelim mdelim]
+[\-\-nproc N] [\-v]
+[INPUT_FILE] [OUTPUT_FILE]
+.SH DESCRIPTION
+.SS MetaPhlAn 2 clade\-abundance estimation
+.PP
+The basic usage of MetaPhlAn 2 consists in the identification of the clades (from phyla to species and
+strains in particular cases) present in the metagenome obtained from a microbiome sample and their
+relative abundance. This correspond to the default analysis type (\fB\-\-analysis_type\fR rel_ab).
+.IP *
+Profiling a metagenome from raw reads:
+.IP
+metaphlan2 metagenome.fastq \fB\-\-input_type\fR fastq
+.IP *
+You can take advantage of multiple CPUs and save the intermediate BowTie2 output for re\-running
+.IP
+MetaPhlAn extremely quickly:
+.br
+metaphlan2 metagenome.fastq \fB\-\-bowtie2out\fR metagenome.bowtie2.bz2 \fB\-\-nproc\fR 5 \fB\-\-input_type\fR fastq
+.IP *
+If you already mapped your metagenome against the marker DB (using a previous MetaPhlAn run), you
+can obtain the results in few seconds by using the previously saved \fB\-\-bowtie2out\fR file and
+specifying the input (\fB\-\-input_type\fR bowtie2out):
+.IP
+metaphlan2 metagenome.bowtie2.bz2 \fB\-\-nproc\fR 5 \fB\-\-input_type\fR bowtie2out
+.IP *
+You can also provide an externally BowTie2\-mapped SAM if you specify this format with
+\fB\-\-input_type\fR. Two steps: first apply BowTie2 and then feed MetaPhlAn2 with the obtained sam:
+.IP
+bowtie2 \fB\-\-sam\-no\-hd\fR \fB\-\-sam\-no\-sq\fR \fB\-\-no\-unal\fR \fB\-\-very\-sensitive\fR \fB\-S\fR metagenome.sam \fB\-x\fR ${mpa_dir}/db_v20/mpa_v20_m200 \fB\-U\fR metagenome.fastq
+metaphlan2 metagenome.sam \fB\-\-input_type\fR sam > profiled_metagenome.txt
+.IP *
+Multiple alternative ways to pass the input are also available:
+.IP
+cat metagenome.fastq | metaphlan2 \fB\-\-input_type\fR fastq
+.br
+tar xjf metagenome.tar.bz2 \fB\-\-to\-stdout\fR | metaphlan2 \fB\-\-input_type\fR fastq
+.br
+metaphlan2 \fB\-\-input_type\fR fastq < metagenome.fastq
+.br
+metaphlan2 \fB\-\-input_type\fR fastq <(bzcat metagenome.fastq.bz2)
+.br
+metaphlan2 \fB\-\-input_type\fR fastq <(zcat metagenome_1.fastq.gz metagenome_2.fastq.gz)
+.IP *
+We can also natively handle paired\-end metagenomes, and, more generally, metagenomes stored in
+multiple files (but you need to specify the \fB\-\-bowtie2out\fR parameter):
+.IP
+metaphlan2 metagenome_1.fastq,metagenome_2.fastq \fB\-\-bowtie2out\fR metagenome.bowtie2.bz2 \fB\-\-nproc\fR 5 \fB\-\-input_type\fR fastq
+.SS MetaPhlAn 2 strain tracking
+.PP
+MetaPhlAn 2 introduces the capability of charachterizing organisms at the strain level using non
+aggregated marker information. Such capability comes with several slightly different flavours and
+are a way to perform strain tracking and comparison across multiple samples.
+Usually, MetaPhlAn 2 is first ran with the default \fB\-\-analysis_type\fR to profile the species present in
+the community, and then a strain\-level profiling can be performed to zoom\-in into specific species
+of interest. This operation can be performed quickly as it exploits the \fB\-\-bowtie2out\fR intermediate
+file saved during the execution of the default analysis type.
+.IP *
+The following command will output the abundance of each marker with a RPK (reads per kil\-base)
+higher 0.0. (we are assuming that metagenome_outfmt.bz2 has been generated before as
+shown above).
+.IP
+metaphlan2 \fB\-t\fR marker_ab_table metagenome_outfmt.bz2 \fB\-\-input_type\fR bowtie2out > marker_abundance_table.txt
+.IP
+The obtained RPK can be optionally normalized by the total number of reads in the metagenome
+to guarantee fair comparisons of abundances across samples. The number of reads in the metagenome
+needs to be passed with the '\-\-nreads' argument
+.IP *
+The list of markers present in the sample can be obtained with '\-t marker_pres_table'
+.IP
+metaphlan2 \fB\-t\fR marker_pres_table metagenome_outfmt.bz2 \fB\-\-input_type\fR bowtie2out > marker_abundance_table.txt
+.IP
+The \fB\-\-pres_th\fR argument (default 1.0) set the minimum RPK value to consider a marker present
+.IP *
+The list '\-t clade_profiles' analysis type reports the same information of '\-t marker_ab_table'
+but the markers are reported on a clade\-by\-clade basis.
+.IP
+metaphlan2 \fB\-t\fR clade_profiles metagenome_outfmt.bz2 \fB\-\-input_type\fR bowtie2out > marker_abundance_table.txt
+.IP *
+Finally, to obtain all markers present for a specific clade and all its subclades, the
+\&'\-t clade_specific_strain_tracker' should be used. For example, the following command
+is reporting the presence/absence of the markers for the B. fragulis species and its strains
+the optional argument \fB\-\-min_ab\fR specifies the minimum clade abundance for reporting the markers
+.IP
+$ metaphlan2 \fB\-t\fR clade_specific_strain_tracker \fB\-\-clade\fR s__Bacteroides_fragilis metagenome_outfmt.bz2 \fB\-\-input_type\fR bowtie2out > marker_abundance_table.txt
+.PP
+.SH OPTIONS
+.SS positional arguments
+.TP
+INPUT_FILE
+the input file can be:
+.IP *
+a fastq file containing metagenomic reads
+.IP
+OR
+.IP *
+a BowTie2 produced SAM file.
+.IP
+OR
+.IP *
+an intermediary mapping file of the metagenome generated by a previous MetaPhlAn run
+.IP
+If the input file is missing, the script assumes that the input is provided using the standard
+input, or named pipes.
+IMPORTANT: the type of input needs to be specified with \fB\-\-input_type\fR
+.TP
+OUTPUT_FILE
+the tab\-separated output file of the predicted taxon relative abundances
+[stdout if not present]
+.SS Required arguments
+.TP
+\fB\-\-input_type\fR {fastq,fasta,multifasta,multifastq,bowtie2out,sam}
+set whether the input is the multifasta file of metagenomic reads or
+the SAM file of the mapping of the reads against the MetaPhlAn db.
+[default 'automatic', i.e. the script will try to guess the input format]
+.SS "Mapping arguments:"
+.TP
+\fB\-\-mpa_pkl\fR MPA_PKL
+the metadata pickled MetaPhlAn file
+.TP
+\fB\-\-bowtie2db\fR METAPHLAN_BOWTIE2_DB
+The BowTie2 database file of the MetaPhlAn database.
+Used if \fB\-\-input_type\fR is fastq, fasta, multifasta, or multifastq
+.TP
+\fB\-\-bt2_ps\fR BowTie2 presets
+presets options for BowTie2 (applied only when a multifasta file is provided)
+The choices enabled in MetaPhlAn are:
+.IP *
+sensitive
+.IP *
+very\-sensitive
+.IP *
+sensitive\-local
+.IP *
+very\-sensitive\-local
+.IP
+[default very\-sensitive]
+.TP
+\fB\-\-bowtie2_exe\fR BOWTIE2_EXE
+Full path and name of the BowTie2 executable. This option allows
+MetaPhlAn to reach the executable even when it is not in the system
+PATH or the system PATH is unreachable
+.TP
+\fB\-\-bowtie2out\fR FILE_NAME
+The file for saving the output of BowTie2
+.TP
+\fB\-\-no_map\fR
+Avoid storing the \fB\-\-bowtie2out\fR map file
+.TP
+\fB\-\-tmp_dir\fR
+the folder used to store temporary files
+[default is the OS dependent tmp dir]
+.SS Post-mapping arguments
+.TP
+\fB\-\-tax_lev\fR TAXONOMIC_LEVEL
+The taxonomic level for the relative abundance output:
+.br
+\&'a' : all taxonomic levels
+.br
+\&'k' : kingdoms
+.br
+\&'p' : phyla only
+.br
+\&'c' : classes only
+.br
+\&'o' : orders only
+.br
+\&'f' : families only
+.br
+\&'g' : genera only
+.br
+\&'s' : species only
+.br
+[default 'a']
+.TP
+\fB\-\-min_cu_len\fR
+minimum total nucleotide length for the markers in a clade for
+estimating the abundance without considering sub\-clade abundances
+[default 2000]
+.TP
+\fB\-\-min_alignment_len\fR
+The sam records for aligned reads with the longest subalignment
+length smaller than this threshold will be discarded.
+[default None]
+.TP
+\fB\-\-ignore_viruses\fR
+Do not profile viral organisms
+.TP
+\fB\-\-ignore_eukaryotes\fR
+Do not profile eukaryotic organisms
+.TP
+\fB\-\-ignore_bacteria\fR
+Do not profile bacterial organisms
+.TP
+\fB\-\-ignore_archaea\fR
+Do not profile archeal organisms
+.TP
+\fB\-\-stat_q\fR
+Quantile value for the robust average
+[default 0.1]
+.TP
+\fB\-\-ignore_markers\fR IGNORE_MARKERS
+File containing a list of markers to ignore.
+.TP
+\fB\-\-avoid_disqm\fR
+Deactivate the procedure of disambiguating the quasi\-markers based on the
+marker abundance pattern found in the sample. It is generally recommended
+too keep the disambiguation procedure in order to minimize false positives
+.TP
+\fB\-\-stat\fR
+EXPERIMENTAL! Statistical approach for converting marker abundances into clade abundances
+.br
+\&'avg_g' : clade global (i.e. normalizing all markers together) average
+.br
+\&'avg_l' : average of length\-normalized marker counts
+.br
+\&'tavg_g' : truncated clade global average at \fB\-\-stat_q\fR quantile
+.br
+\&'tavg_l' : trunated average of length\-normalized marker counts (at \fB\-\-stat_q\fR)
+.br
+\&'wavg_g' : winsorized clade global average (at \fB\-\-stat_q\fR)
+.br
+\&'wavg_l' : winsorized average of length\-normalized marker counts (at \fB\-\-stat_q\fR)
+.br
+\&'med' : median of length\-normalized marker counts
+.br
+[default tavg_g]
+.SS Additional analysis types and arguments
+.TP
+\fB\-t\fR ANALYSIS TYPE
+Type of analysis to perform:
+.IP *
+rel_ab: profiling a metagenomes in terms of relative abundances
+.IP *
+rel_ab_w_read_stats: profiling a metagenomes in terms of relative abundances and estimate the number of reads coming from each clade.
+.IP *
+reads_map: mapping from reads to clades (only reads hitting a marker)
+.IP *
+clade_profiles: normalized marker counts for clades with at least a non\-null marker
+.IP *
+marker_ab_table: normalized marker counts (only when > 0.0 and normalized by metagenome size if \fB\-\-nreads\fR is specified)
+.IP *
+marker_counts: non\-normalized marker counts [use with extreme caution]
+.IP *
+marker_pres_table: list of markers present in the sample (threshold at 1.0 if not differently specified with \fB\-\-pres_th\fR
+.IP
+[default 'rel_ab']
+.TP
+\fB\-\-nreads\fR NUMBER_OF_READS
+The total number of reads in the original metagenome. It is used only when
+\fB\-t\fR marker_table is specified for normalizing the length\-normalized counts
+with the metagenome size as well. No normalization applied if \fB\-\-nreads\fR is not
+specified
+.TP
+\fB\-\-pres_th\fR PRESENCE_THRESHOLD
+Threshold for calling a marker present by the \fB\-t\fR marker_pres_table option
+.TP
+\fB\-\-clade\fR
+The clade for clade_specific_strain_tracker analysis
+.TP
+\fB\-\-min_ab\fR
+The minimum percentage abundace for the clade in the clade_specific_strain_tracker analysis
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.SS Output arguments
+.TP
+\fB\-o\fR output file, \fB\-\-output_file\fR output file
+The output file (if not specified as positional argument)
+.TP
+\fB\-\-sample_id_key\fR name
+Specify the sample ID key for this analysis. Defaults to '#SampleID'.
+.TP
+\fB\-\-sample_id\fR value
+Specify the sample ID for this analysis. Defaults to 'Metaphlan2_Analysis'.
+.TP
+\fB\-s\fR sam_output_file, \fB\-\-samout\fR sam_output_file
+The sam output file
+.TP
+\fB\-\-biom\fR biom_output, \fB\-\-biom_output_file\fR biom_output
+If requesting biom file output: The name of the output file in biom format
+.TP
+\fB\-\-mdelim\fR mdelim, \fB\-\-metadata_delimiter_char\fR mdelim
+Delimiter for bug metadata: \- defaults to pipe. e.g. the pipe in k__Bacteria|p__Proteobacteria
+.SS Other arguments
+.TP
+\fB\-\-nproc\fR N
+The number of CPUs to use for parallelizing the mapping
+[default 1, i.e. no parallelism]
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+Prints the current MetaPhlAn version and exit
+.SH AUTHOR
+The code of MetaPhlAn was rwitten by Nicola Segata (nicola.segata at unitn.it), Duy Tin Truong (duytin.truong at unitn.it).
+.P
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
Added: trunk/packages/metaphlan2/trunk/debian/metaphlan2_strainer.1
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/metaphlan2_strainer.1 (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/metaphlan2_strainer.1 2016-07-25 14:40:21 UTC (rev 22630)
@@ -0,0 +1,209 @@
+.TH METAPHLAN2_STRAINER "1" "July 2016" "metaphlan2_strainer 2.5.0" "User Commands"
+.SH NAME
+metaphlan2_strainer \- METAgenomic PHyLogenetic ANalysis for metagenomic taxonomic profiling (strainer)
+.SH SYNOPSIS
+.B metaphlan2_strainer.py
+[\-h] \fB\-\-ifn_samples\fR IFN_SAMPLES [IFN_SAMPLES ...]
+\fB\-\-mpa_pkl\fR MPA_PKL \fB\-\-output_dir\fR OUTPUT_DIR
+[\-\-ifn_markers IFN_MARKERS]
+[\-\-nprocs_main NPROCS_MAIN]
+[\-\-nprocs_load_samples NPROCS_LOAD_SAMPLES]
+[\-\-nprocs_align_clean NPROCS_ALIGN_CLEAN]
+[\-\-nprocs_raxml NPROCS_RAXML]
+[\-\-bootstrap_raxml BOOTSTRAP_RAXML]
+[\-\-ifn_ref_genomes IFN_REF_GENOMES [IFN_REF_GENOMES ...]]
+[\-\-N_in_marker N_IN_MARKER]
+[\-\-marker_strip_length MARKER_STRIP_LENGTH]
+[\-\-marker_in_clade MARKER_IN_CLADE]
+[\-\-sample_in_clade SAMPLE_IN_CLADE]
+[\-\-sample_in_marker SAMPLE_IN_MARKER]
+[\-\-gap_in_trailing_col GAP_IN_TRAILING_COL]
+[\-\-gap_trailing_col_limit GAP_TRAILING_COL_LIMIT]
+[\-\-gap_in_internal_col GAP_IN_INTERNAL_COL]
+[\-\-gap_in_sample GAP_IN_SAMPLE] [\-\-N_col N_COL]
+[\-\-N_count N_COUNT]
+[\-\-long_gap_length LONG_GAP_LENGTH]
+[\-\-long_gap_percentage LONG_GAP_PERCENTAGE]
+[\-\-p_value P_VALUE]
+[\-\-clades CLADES [CLADES ...]]
+[\-\-marker_list_fn MARKER_LIST_FN]
+[\-\-print_clades_only]
+[\-\-alignment_program {muscle,mafft}]
+[\-\-relaxed_parameters] [\-\-relaxed_parameters2]
+[\-\-keep_alignment_files]
+[\-\-keep_full_alignment_files]
+[\-\-save_sample2fullfreq] [\-\-use_threads]
+.SH DESCRIPTION
+Metaphlan2_strainer is a computational tool for tracking individual strains
+across large set of samples. The input of metaphlan2_strainer is a set of
+metagenomic samples and the output is a set of phylogenetic.
+.
+For each sample, metaphlan2_strainer extracts the strain of a specific species
+by merging and concatenating all reads mapped against that species markers in
+the MetaPhlAn2 database.
+.SH OPTIONS
+.SS optional arguments
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-ifn_samples\fR IFN_SAMPLES [IFN_SAMPLES ...]
+The list of sample files (space separated).The
+wildcard can also be used.
+.TP
+\fB\-\-mpa_pkl\fR MPA_PKL
+The database of metaphlan3.py.
+.TP
+\fB\-\-output_dir\fR OUTPUT_DIR
+The output directory.
+.TP
+\fB\-\-ifn_markers\fR IFN_MARKERS
+The marker file in fasta format.
+.TP
+\fB\-\-nprocs_main\fR NPROCS_MAIN
+The number of processors are used for the main
+threads. Default 1.
+.TP
+\fB\-\-nprocs_load_samples\fR NPROCS_LOAD_SAMPLES
+The number of processors are used for loading samples.
+Default nprocs_main.
+.TP
+\fB\-\-nprocs_align_clean\fR NPROCS_ALIGN_CLEAN
+The number of processors are used for aligning and
+cleaning markers. Default nprocs_main.
+.TP
+\fB\-\-nprocs_raxml\fR NPROCS_RAXML
+The number of processors are used for running raxml.
+Default nprocs_main.
+.TP
+\fB\-\-bootstrap_raxml\fR BOOTSTRAP_RAXML
+The number of runs for bootstraping when building the
+tree. Default 0.
+.TP
+\fB\-\-ifn_ref_genomes\fR IFN_REF_GENOMES [IFN_REF_GENOMES ...]
+The reference genome file names. They are separated by
+spaces.
+.TP
+\fB\-\-N_in_marker\fR N_IN_MARKER
+The consensus markers with the rate of N nucleotides
+greater than this threshold are removed. Default 0.2.
+.TP
+\fB\-\-marker_strip_length\fR MARKER_STRIP_LENGTH
+The number of nucleotides will be deleted from each of
+two ends of a marker. Default 50.
+.TP
+\fB\-\-marker_in_clade\fR MARKER_IN_CLADE
+In each sample, the clades with the rate of present
+markers less than this threshold are removed. Default
+0.8.
+.TP
+\fB\-\-sample_in_clade\fR SAMPLE_IN_CLADE
+Only clades present in at least sample_in_clade
+samples are kept. Default 2.
+.TP
+\fB\-\-sample_in_marker\fR SAMPLE_IN_MARKER
+If the percentage of samples that a marker present in
+is less than this threshold, that marker is removed.
+Default 0.8.
+.TP
+\fB\-\-gap_in_trailing_col\fR GAP_IN_TRAILING_COL
+If the number of the trailing nucleotide columns in
+aligned markers with the percentage of gaps greater
+than gap_in_trailing_col is less than
+gap_trailing_col_limit, these columns will be removed.
+Default 0.2.
+.TP
+\fB\-\-gap_trailing_col_limit\fR GAP_TRAILING_COL_LIMIT
+If the number of the trailing nucleotide columns in
+aligned markers with the percentage of gaps greater
+than gap_in_trailing_col is less than
+gap_trailing_col_limit, these columns will be removed.
+Default 101.
+.TP
+\fB\-\-gap_in_internal_col\fR GAP_IN_INTERNAL_COL
+The internal nucleotide columns in aligned markers
+with the percentage of gaps greater than
+gap_in_internal_col will be removed. Default 0.3.
+.TP
+\fB\-\-gap_in_sample\fR GAP_IN_SAMPLE
+The samples with full sequences from all markers and
+having the percentage of gaps greater than this
+threshold will be removed. Default 0.2.
+.TP
+\fB\-\-N_col\fR N_COL
+In aligned markers, if the percentage of nucleotide
+columns containing more than N_count Ns less than this
+threshold, these columns will be removed. Default 0.8.
+.TP
+\fB\-\-N_count\fR N_COUNT
+In aligned markers, if the percentage of nucleotide
+columns containing more than N_count Ns less than
+N_col threshold, these columns will be removed.
+Default 0.
+.TP
+\fB\-\-long_gap_length\fR LONG_GAP_LENGTH
+In each concatenated sequence of a sample, sequential
+gap positions is a gap group. A gap group with length
+greater than this threshold is considered as a long
+gap group. If the ratio between the number of unique
+positions in all long gap groups and the concatenated
+sequence length is less than long_gap_percentage,
+these positions will be removed from all concatenated
+sequences. Default 2.
+.TP
+\fB\-\-long_gap_percentage\fR LONG_GAP_PERCENTAGE
+Combining this threshold with long_gap_length to
+removed long gaps. Default 0.8.
+.TP
+\fB\-\-p_value\fR P_VALUE
+The p_value to reject a non\-polymorphic site.Default
+0.05.
+.TP
+\fB\-\-clades\fR CLADES [CLADES ...]
+The clades (space seperated) for which the script will
+compute the marker alignments in fasta format and the
+phylogenetic trees. If a file name is specified, the
+clade list in that file where each clade name is on a
+line will be read.Default "automatically identify all
+clades".
+.TP
+\fB\-\-marker_list_fn\fR MARKER_LIST_FN
+The file name containing the list of considered
+markers. The other markers will be discarded. Default
+"None".
+.TP
+\fB\-\-print_clades_only\fR
+Only print the potential clades and stop without
+building any tree. This option is useful when you want
+to check quickly all possible clades and rerun only
+for some specific ones. Default "False".
+.TP
+\fB\-\-alignment_program\fR {muscle,mafft}
+The alignment program. Default "muscle".
+.TP
+\fB\-\-relaxed_parameters\fR
+Set marker_in_clade=0.5, sample_in_marker=0.5,
+N_in_marker=0.5, gap_in_sample=0.5. Default "False".
+.TP
+\fB\-\-relaxed_parameters2\fR
+Set marker_in_clade=0.2, sample_in_marker=0.2,
+N_in_marker=0.8, gap_in_sample=0.8. Default "False".
+.TP
+\fB\-\-keep_alignment_files\fR
+Keep the alignment files of all markers before
+cleaning step.
+.TP
+\fB\-\-keep_full_alignment_files\fR
+Keep the alignment files of all markers before
+truncating the starting and ending parts, and cleaning
+step. This is equivalent to \fB\-\-keep_alignment_files\fR
+\fB\-\-marker_strip_length\fR 0
+.TP
+\fB\-\-save_sample2fullfreq\fR
+Save sample2fullfreq to a msgpack file
+sample2fullfreq.msgpack.
+.TP
+\fB\-\-use_threads\fR
+Use multithreading. Default "Use multiprocessing".
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
Added: trunk/packages/metaphlan2/trunk/debian/patches/fix_sequence.patch
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/patches/fix_sequence.patch (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/patches/fix_sequence.patch 2016-07-25 14:40:21 UTC (rev 22630)
@@ -0,0 +1,22 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 23 May 2016 16:09:13 +0200
+Description: Make sure shebang line is first of file
+
+--- a/strainer_src/add_metadata.py
++++ b/strainer_src/add_metadata.py
+@@ -1,5 +1,5 @@
+-#Author: Duy Tin Truong (duytin.truong at unitn.it)
+ #!/usr/bin/env python
++#Author: Duy Tin Truong (duytin.truong at unitn.it)
+ # at CIBIO, University of Trento, Italy
+
+
+--- a/metaphlan2_strainer.py
++++ b/metaphlan2_strainer.py
+@@ -1,5 +1,5 @@
+-# Author: Duy Tin Truong (duytin.truong at unitn.it)
+ #!/usr/bin/env python
++# Author: Duy Tin Truong (duytin.truong at unitn.it)
+ # at CIBIO, University of Trento, Italy
+
+ __author__ = 'Duy Tin Truong (duytin.truong at unitn.it)'
Added: trunk/packages/metaphlan2/trunk/debian/patches/mpa_dir-is-usr_share_metaphlan2.patch
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/patches/mpa_dir-is-usr_share_metaphlan2.patch (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/patches/mpa_dir-is-usr_share_metaphlan2.patch 2016-07-25 14:40:21 UTC (rev 22630)
@@ -0,0 +1,233 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 23 May 2016 16:09:13 +0200
+Description: Instead of setting mpa_dir bash variable the path to the
+ database files in /usr/share/metahplan2 is set explicitly.
+ .
+ The doc is also adapted to this change.
+
+--- a/metaphlan2.py
++++ b/metaphlan2.py
+@@ -386,7 +386,7 @@ def read_params(args):
+
+ "* You can also provide an externally BowTie2-mapped SAM if you specify this format with \n"
+ " --input_type. Two steps: first apply BowTie2 and then feed MetaPhlAn2 with the obtained sam:\n"
+- "$ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x ${mpa_dir}/db_v20/mpa_v20_m200 -U metagenome.fastq\n"
++ "$ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x /usr/share/metahplan2/db_v20/mpa_v20_m200 -U metagenome.fastq\n"
+ "$ metaphlan2.py metagenome.sam --input_type sam > profiled_metagenome.txt\n\n"
+
+ "* Multiple alternative ways to pass the input are also available:\n"
+@@ -1104,7 +1104,7 @@ if __name__ == '__main__':
+ # check for the mpa_pkl file
+ if not os.path.isfile(pars['mpa_pkl']):
+ sys.stderr.write("Error: Unable to find the mpa_pkl file at: " + pars['mpa_pkl'] +
+- "\nExpecting location ${mpa_dir}/db_v20/map_v20_m200.pkl "
++ "\nExpecting location /usr/share/metahplan2/db_v20/map_v20_m200.pkl "
+ "\nSelect the file location with the option --mpa_pkl.\n"
+ "Exiting...\n\n")
+ sys.exit(1)
+@@ -1152,7 +1152,7 @@ if __name__ == '__main__':
+ sys.stderr.write( "No MetaPhlAn BowTie2 database found "
+ "[--bowtie2db option]! "
+ "(or wrong path provided)."
+- "\nExpecting location ${mpa_dir}/db_v20/map_v20_m200 "
++ "\nExpecting location /usr/share/metahplan2/db_v20/map_v20_m200 "
+ "\nExiting... " )
+ sys.exit(1)
+
+--- a/README.md
++++ b/README.md
+@@ -60,74 +60,69 @@ Cloning the repository via the following
+
+ This section presents some basic usages of MetaPhlAn2, for more advanced usages, please see at [its wiki](https://bitbucket.org/biobakery/biobakery/wiki/metaphlan2).
+
+-We assume here that ``metaphlan2.py`` is in the system path and that ``mpa_dir`` bash variable contains the main MetaPhlAn folder. You can set this two variables moving to your MetaPhlAn2 local folder and type:
++We assume here that ``metaphlan2`` is in the system path.
+ ```
+-#!cmd
+-$ export PATH=`pwd`:$PATH
+-$ export mpa_dir=`pwd`
+-```
+-
+ Here is the basic example to profile a metagenome from raw reads (requires BowTie2 in the system path with execution and read permissions, Perl installed).
+
+ ```
+ #!cmd
+-$ metaphlan2.py metagenome.fastq --input_type fastq > profiled_metagenome.txt
++$ metaphlan2 metagenome.fastq --input_type fastq > profiled_metagenome.txt
+ ```
+
+ It is highly recommended to save the intermediate BowTie2 output for re-running MetaPhlAn extremely quickly (--bowtie2out), and use multiple CPUs (--nproc) if available:
+
+ ```
+ #!cmd
+-$ metaphlan2.py metagenome.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq > profiled_metagenome.txt
++$ metaphlan2 metagenome.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq > profiled_metagenome.txt
+ ```
+
+ If you already mapped your metagenome against the marker DB (using a previous MetaPhlAn run), you can obtain the results in few seconds by using the previously saved --bowtie2out file and specifying the input (--input_type bowtie2out):
+
+ ```
+ #!cmd
+-$ metaphlan2.py metagenome.bowtie2.bz2 --nproc 5 --input_type bowtie2out > profiled_metagenome.txt
++$ metaphlan2 metagenome.bowtie2.bz2 --nproc 5 --input_type bowtie2out > profiled_metagenome.txt
+ ```
+
+ You can also provide an externally BowTie2-mapped SAM if you specify this format with --input_type. Two steps here: first map your metagenome with BowTie2 and then feed MetaPhlAn2 with the obtained sam:
+
+ ```
+ #!cmd
+-$ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x ${mpa_dir}/db_v20/mpa_v20_m200 -U metagenome.fastq
+-$ metaphlan2.py metagenome.sam --input_type sam > profiled_metagenome.txt
++$ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x /usr/share/metahplan2/db_v20/mpa_v20_m200 -U metagenome.fastq
++$ metaphlan2 metagenome.sam --input_type sam > profiled_metagenome.txt
+ ```
+
+ In order to make MetaPhlAn 2 easily compatible with complex metagenomic pipeline, there are now multiple alternative ways to pass the input:
+
+ ```
+ #!cmd
+-$ cat metagenome.fastq | metaphlan2.py --input_type fastq > profiled_metagenome.txt
++$ cat metagenome.fastq | metaphlan2 --input_type fastq > profiled_metagenome.txt
+ ```
+
+ ```
+ #!cmd
+-$ tar xjf metagenome.tar.bz2 --to-stdout | metaphlan2.py --input_type fastq --bowtie2db ${mpa_dir}/db_v20/mpa_v20_m200 > profiled_metagenome.txt
++$ tar xjf metagenome.tar.bz2 --to-stdout | metaphlan2 --input_type fastq --bowtie2db /usr/share/metahplan2/db_v20/mpa_v20_m200 > profiled_metagenome.txt
+ ```
+
+ ```
+ #!cmd
+-$ metaphlan2.py --input_type fastq < metagenome.fastq > profiled_metagenome.txt
++$ metaphlan2 --input_type fastq < metagenome.fastq > profiled_metagenome.txt
+ ```
+
+ ```
+ #!cmd
+-$ metaphlan2.py --input_type fastq <(bzcat metagenome.fastq.bz2) > profiled_metagenome.txt
++$ metaphlan2 --input_type fastq <(bzcat metagenome.fastq.bz2) > profiled_metagenome.txt
+ ```
+
+ ```
+ #!cmd
+-$ metaphlan2.py --input_type fastq <(zcat metagenome_1.fastq.gz metagenome_2.fastq.gz) > profiled_metagenome.txt
++$ metaphlan2 --input_type fastq <(zcat metagenome_1.fastq.gz metagenome_2.fastq.gz) > profiled_metagenome.txt
+ ```
+
+ MetaPhlAn 2 can also natively **handle paired-end metagenomes**, and, more generally, metagenomes stored in multiple files (but you need to specify the --bowtie2out parameter):
+
+ ```
+ #!cmd
+-$ metaphlan2.py metagenome_1.fastq,metagenome_2.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq > profiled_metagenome.txt
++$ metaphlan2 metagenome_1.fastq,metagenome_2.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq > profiled_metagenome.txt
+ ```
+
+ For advanced options and other analysis types (such as strain tracking) please refer to the full command-line options.
+@@ -136,7 +131,7 @@ For advanced options and other analysis
+
+
+ ```
+-usage: metaphlan2.py --input_type
++usage: metaphlan2 --input_type
+ {fastq,fasta,multifasta,multifastq,bowtie2out,sam}
+ [--mpa_pkl MPA_PKL] [--bowtie2db METAPHLAN_BOWTIE2_DB]
+ [--bt2_ps BowTie2 presets] [--bowtie2_exe BOWTIE2_EXE]
+@@ -161,7 +156,7 @@ AUTHORS: Nicola Segata (nicola.segata at un
+
+ COMMON COMMANDS
+
+- We assume here that metaphlan2.py is in the system path and that mpa_dir bash variable contains the
++ We assume here that metaphlan2 is in the system path and that mpa_dir bash variable contains the
+ main MetaPhlAn folder. Also BowTie2 should be in the system path with execution and read
+ permissions, and Perl should be installed.
+
+@@ -172,32 +167,32 @@ strains in particular cases) present in
+ relative abundance. This correspond to the default analysis type (--analysis_type rel_ab).
+
+ * Profiling a metagenome from raw reads:
+-$ metaphlan2.py metagenome.fastq --input_type fastq
++$ metaphlan2 metagenome.fastq --input_type fastq
+
+ * You can take advantage of multiple CPUs and save the intermediate BowTie2 output for re-running
+ MetaPhlAn extremely quickly:
+-$ metaphlan2.py metagenome.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq
++$ metaphlan2 metagenome.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq
+
+ * If you already mapped your metagenome against the marker DB (using a previous MetaPhlAn run), you
+ can obtain the results in few seconds by using the previously saved --bowtie2out file and
+ specifying the input (--input_type bowtie2out):
+-$ metaphlan2.py metagenome.bowtie2.bz2 --nproc 5 --input_type bowtie2out
++$ metaphlan2 metagenome.bowtie2.bz2 --nproc 5 --input_type bowtie2out
+
+ * You can also provide an externally BowTie2-mapped SAM if you specify this format with
+ --input_type. Two steps: first apply BowTie2 and then feed MetaPhlAn2 with the obtained sam:
+-$ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x ${mpa_dir}/db_v20/mpa_v20_m200 -U metagenome.fastq
+-$ metaphlan2.py metagenome.sam --input_type sam > profiled_metagenome.txt
++$ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x /usr/share/metahplan2/db_v20/mpa_v20_m200 -U metagenome.fastq
++$ metaphlan2 metagenome.sam --input_type sam > profiled_metagenome.txt
+
+ * Multiple alternative ways to pass the input are also available:
+-$ cat metagenome.fastq | metaphlan2.py --input_type fastq
+-$ tar xjf metagenome.tar.bz2 --to-stdout | metaphlan2.py --input_type fastq
+-$ metaphlan2.py --input_type fastq < metagenome.fastq
+-$ metaphlan2.py --input_type fastq <(bzcat metagenome.fastq.bz2)
+-$ metaphlan2.py --input_type fastq <(zcat metagenome_1.fastq.gz metagenome_2.fastq.gz)
++$ cat metagenome.fastq | metaphlan2 --input_type fastq
++$ tar xjf metagenome.tar.bz2 --to-stdout | metaphlan2 --input_type fastq
++$ metaphlan2 --input_type fastq < metagenome.fastq
++$ metaphlan2 --input_type fastq <(bzcat metagenome.fastq.bz2)
++$ metaphlan2 --input_type fastq <(zcat metagenome_1.fastq.gz metagenome_2.fastq.gz)
+
+ * We can also natively handle paired-end metagenomes, and, more generally, metagenomes stored in
+ multiple files (but you need to specify the --bowtie2out parameter):
+-$ metaphlan2.py metagenome_1.fastq,metagenome_2.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq
++$ metaphlan2 metagenome_1.fastq,metagenome_2.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq
+
+ -------------------------------------------------------------------
+
+@@ -215,23 +210,23 @@ file saved during the execution of the d
+ * The following command will output the abundance of each marker with a RPK (reads per kil-base)
+ higher 0.0. (we are assuming that metagenome_outfmt.bz2 has been generated before as
+ shown above).
+-$ metaphlan2.py -t marker_ab_table metagenome_outfmt.bz2 --input_type bowtie2out > marker_abundance_table.txt
++$ metaphlan2 -t marker_ab_table metagenome_outfmt.bz2 --input_type bowtie2out > marker_abundance_table.txt
+ The obtained RPK can be optionally normalized by the total number of reads in the metagenome
+ to guarantee fair comparisons of abundances across samples. The number of reads in the metagenome
+ needs to be passed with the '--nreads' argument
+
+ * The list of markers present in the sample can be obtained with '-t marker_pres_table'
+-$ metaphlan2.py -t marker_pres_table metagenome_outfmt.bz2 --input_type bowtie2out > marker_abundance_table.txt
++$ metaphlan2 -t marker_pres_table metagenome_outfmt.bz2 --input_type bowtie2out > marker_abundance_table.txt
+ The --pres_th argument (default 1.0) set the minimum RPK value to consider a marker present
+
+ * The list '-t clade_profiles' analysis type reports the same information of '-t marker_ab_table'
+ but the markers are reported on a clade-by-clade basis.
+-$ metaphlan2.py -t clade_profiles metagenome_outfmt.bz2 --input_type bowtie2out > marker_abundance_table.txt
++$ metaphlan2 -t clade_profiles metagenome_outfmt.bz2 --input_type bowtie2out > marker_abundance_table.txt
+
+ * Finally, to obtain all markers present for a specific clade and all its subclades, the
+ '-t clade_specific_strain_tracker' should be used. For example, the following command
+ is reporting the presence/absence of the markers for the B. fragulis species and its strains
+-$ metaphlan2.py -t clade_specific_strain_tracker --clade s__Bacteroides_fragilis metagenome_outfmt.bz2 db_v20/mpa_v20_m200.pkl --input_type bowtie2out > marker_abundance_table.txt
++$ metaphlan2 -t clade_specific_strain_tracker --clade s__Bacteroides_fragilis metagenome_outfmt.bz2 db_v20/mpa_v20_m200.pkl --input_type bowtie2out > marker_abundance_table.txt
+ the optional argument --min_ab specifies the minimum clade abundance for reporting the markers
+
+ -------------------------------------------------------------------
+@@ -537,7 +532,7 @@ pickle.dump(db, ofile, pickle.HIGHEST_PR
+ ofile.close()
+ ```
+
+-* To use the new database, switch to metaphlan2/db_v21 instead of metaphlan2/db_v20 when running metaphlan2.py with option "--mpa_pkl".
++* To use the new database, switch to metaphlan2/db_v21 instead of metaphlan2/db_v20 when running metaphlan2 with option "--mpa_pkl".
+
+
+ ##**Metagenomic strain-level population genomics**##
+@@ -611,7 +606,7 @@ for f in $(ls fastqs/*.bz2)
+ do
+ echo "Running metaphlan2 on ${f}"
+ bn=$(basename ${f} | cut -d . -f 1)
+- tar xjfO ${f} | ../metaphlan2.py --bowtie2db ../db_v20/mpa_v20_m200 --mpa_pkl ../db_v20/mpa_v20_m200.pkl --input_type multifastq --nproc 10 -s sams/${bn}.sam.bz2 --bowtie2out sams/${bn}.bowtie2_out.bz2 -o sams/${bn}.profile
++ tar xjfO ${f} | metaphlan2 --bowtie2db /usr/share/metahplan2/db_v20/mpa_v20_m200 --mpa_pkl /usr/share/metahplan2/db_v20/mpa_v20_m200.pkl --input_type multifastq --nproc 10 -s sams/${bn}.sam.bz2 --bowtie2out sams/${bn}.bowtie2_out.bz2 -o sams/${bn}.profile
+ done
+ ```
+
Added: trunk/packages/metaphlan2/trunk/debian/patches/series
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/patches/series (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/patches/series 2016-07-25 14:40:21 UTC (rev 22630)
@@ -0,0 +1,2 @@
+fix_sequence.patch
+mpa_dir-is-usr_share_metaphlan2.patch
Modified: trunk/packages/metaphlan2/trunk/debian/rules
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/rules 2016-07-25 12:47:08 UTC (rev 22629)
+++ trunk/packages/metaphlan2/trunk/debian/rules 2016-07-25 14:40:21 UTC (rev 22630)
@@ -3,7 +3,17 @@
# DH_VERBOSE := 1
export LC_ALL=C.UTF-8
-
%:
dh $@ --with python2
+override_dh_auto_build:
+ dh_auto_build
+ markdown_py -f README.html README.md
+
+override_dh_installchangelogs:
+ dh_installchangelogs changeset.txt
+
+override_dh_fixperms:
+ dh_fixperms
+ chmod +x debian/*/usr/share/metaphlan2/strainer_tutorial/*.sh
+ chmod -x debian/*/usr/share/metaphlan2/strainer_src/*.ini
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