[med-svn] [Git][med-team/sepp][master] 13 commits: Solving build-test issues with 2 patches to be forwarded upstream
Pierre Gruet
gitlab at salsa.debian.org
Wed Oct 7 21:29:45 BST 2020
Pierre Gruet pushed to branch master at Debian Med / sepp
Commits:
682b41e7 by Pierre Gruet at 2020-10-05T17:42:00+02:00
Solving build-test issues with 2 patches to be forwarded upstream
- - - - -
bafd4b3d by Pierre Gruet at 2020-10-05T17:43:14+02:00
Putting the helper script split_sequences.py in a subdirectory of /usr/share
- - - - -
19f09a53 by Pierre Gruet at 2020-10-06T18:10:41+02:00
Writing manpages and including them in the package
Tiny hack in debian/rules in order to install manpages in /usr/share/man/man1
and not in a py/ directory.
- - - - -
aa66516c by Pierre Gruet at 2020-10-06T21:07:39+02:00
Changing configuration file name from main.config to sepp.config
- - - - -
799584eb by Pierre Gruet at 2020-10-06T21:08:16+02:00
Deleting main.config
- - - - -
eff2c66f by Pierre Gruet at 2020-10-06T22:06:49+02:00
Updating debian/copyright
- - - - -
a274be90 by Pierre Gruet at 2020-10-06T22:08:04+02:00
Providing readmes and tutorials in /usr/share/doc/sepp
- - - - -
4aace3a3 by Pierre Gruet at 2020-10-07T21:19:55+02:00
Invoking python3 instead of python3.8
- - - - -
551e1658 by Pierre Gruet at 2020-10-07T21:33:22+02:00
Proofreading manpages
- - - - -
e899bfdf by Pierre Gruet at 2020-10-07T21:33:57+02:00
Adding autopkgtests
- - - - -
e71fa1bf by Pierre Gruet at 2020-10-07T22:15:34+02:00
Forwarding patches
- - - - -
b5b9c9e5 by Pierre Gruet at 2020-10-07T22:16:29+02:00
Marking Python interpreter as python3 in shebangs
- - - - -
f625ecdf by Pierre Gruet at 2020-10-07T22:18:29+02:00
Deleting useless paragraph in debian/copyright
- - - - -
27 changed files:
- debian/changelog
- debian/copyright
- debian/docs
- debian/install
- + debian/man/run_abundance.py.1
- + debian/man/run_sepp.py.1
- + debian/man/run_tipp.py.1
- + debian/man/run_tipp_tool.py.1
- + debian/man/run_upp.py.1
- + debian/man/sepp.config.5
- + debian/man/tipp.config.5
- + debian/man/upp.config.5
- debian/patches/change_java_version_for_ant.patch
- + debian/patches/deactivating_log_test.patch
- debian/patches/json_collections.patch
- + debian/patches/looking_for_integer_in_placements.patch
- + debian/patches/make_split_sequences_script.patch
- debian/patches/series
- debian/patches/setup.patch
- debian/patches/use_debian_packaged_guppy_from_pplacer.patch
- debian/patches/use_etc_configuration_files.patch
- + debian/patches/using_python3_interpreter.patch
- debian/rules
- + debian/sepp.manpages
- + debian/tests/control
- + debian/tests/run-build-tests
- + debian/tests/test-simple-sepp-call
Changes:
=====================================
debian/changelog
=====================================
@@ -1,10 +1,5 @@
sepp (4.3.10+dfsg-1) UNRELEASED; urgency=medium
* Initial release (Closes: #<bug>)
- TODO:
- - See if split_sequences.py should be shipped.
- - Debug build-time.
- - Write manpages.
- - Write autopkgtests.
- -- Pierre Gruet <pgtdebian at free.fr> Sat, 26 Sep 2020 11:05:33 +0200
+ -- Pierre Gruet <pgtdebian at free.fr> Wed, 07 Oct 2020 21:32:48 +0200
=====================================
debian/copyright
=====================================
@@ -5,30 +5,18 @@ Files-Excluded: tools/bundled
*/*.jar
Files: *
-Copyright: 20xx-20yy <upstream>
-License: GPL-3
+Copyright: 2012, 2014, Siavash Mirarab, Nam Nguyen, and Tandy Warnow.
+License: GPL-3+
-Files: tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/*
-Copyright: Copyright (c) 2012 Rice University
+Files: tools/*
+Copyright: 2012 Rice University
License: GPL-3+
Files: debian/*
Copyright: 2020 Andreas Tille <tille at debian.org>
+ 2020 Pierre Gruet <pgtdebian at ree.fr>
License: GPL-3+
-License: GPL-3
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, version 3 of the License.
- .
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
- .
- On Debian systems you can find the full text of the GNU General Public
- License at /usr/share/common-licenses/GPL-3.
-
License: GPL-3+
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
=====================================
debian/docs
=====================================
@@ -1 +1,6 @@
-README*
+README.SEPP.md
+README.TIPP.md
+README.UPP.md
+tutorial/sepp-tutorial.md
+tutorial/tipp-tutorial.md
+tutorial/upp-tutorial.md
=====================================
debian/install
=====================================
@@ -1,4 +1,4 @@
-main.config etc/sepp
+sepp.config etc/sepp
tipp.config etc/sepp
upp.config etc/sepp
tools/merge/*JsonMerger.jar usr/share/sepp/
=====================================
debian/man/run_abundance.py.1
=====================================
@@ -0,0 +1,149 @@
+.TH RUN_ABUNDANCE.PY "1" "October 2020" "run_abundance.py 4.3.10" "User Commands"
+.SH NAME
+run_abundance.py \- helper script to estimate the abundance at a given taxonomic level
+.SH DESCRIPTION
+usage: run_abundance.py [\-h] [\-v] [\-A N] [\-P N] [\-F N] [\-\-distance DISTANCE]
+.TP
+[\-M DIAMETER] [\-S DECOMP] [\-p DIR] [\-o OUTPUT]
+[\-d OUTPUT_DIR] [\-c CONFIG] [\-t TREE] [\-r RAXML]
+[\-a ALIGN] [\-f FRAG] [\-m MOLECULE] [\-x N]
+[\-cp CHCK_FILE] [\-cpi N] [\-seed N] [\-at N] [\-pt N]
+[\-g N] [\-b N] [\-bin N] [\-D] [\-C N] [\-G GENES]
+.PP
+This script runs the SEPP algorithm on an input tree, alignment, fragment
+file, and RAxML info file.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+show program's version number and exit
+.SS "DECOMPOSITION OPTIONS:"
+.IP
+These options determine the alignment decomposition size and taxon
+insertion size. If None is given, then the default is to align/place at
+10% of total taxa. The alignment decomosition size must be less than the
+taxon insertion size.
+.TP
+\fB\-A\fR N, \fB\-\-alignmentSize\fR N
+max alignment subset size of N [default: 10% of the
+total number of taxa or the placement subset size if
+given]
+.TP
+\fB\-P\fR N, \fB\-\-placementSize\fR N
+max placement subset size of N [default: 10% of the
+total number of taxa or the alignment length
+(whichever bigger)]
+.TP
+\fB\-F\fR N, \fB\-\-fragmentChunkSize\fR N
+maximum fragment chunk size of N. Helps controlling
+memory. [default: 20000]
+.TP
+\fB\-\-distance\fR DISTANCE
+minimum p\-distance before stopping the
+decomposition[default: 1]
+.TP
+\fB\-M\fR DIAMETER, \fB\-\-diameter\fR DIAMETER
+maximum tree diameter before stopping the
+decomposition[default: None]
+.TP
+\fB\-S\fR DECOMP, \fB\-\-decomp_strategy\fR DECOMP
+decomposition strategy [default: using tree branch
+length]
+.SS "OUTPUT OPTIONS:"
+.IP
+These options control output.
+.TP
+\fB\-p\fR DIR, \fB\-\-tempdir\fR DIR
+Tempfile files will be written to DIR. Full\-path
+required. [default: /tmp/sepp]
+.TP
+\fB\-o\fR OUTPUT, \fB\-\-output\fR OUTPUT
+output files with prefix OUTPUT. [default: output]
+.TP
+\fB\-d\fR OUTPUT_DIR, \fB\-\-outdir\fR OUTPUT_DIR
+output to OUTPUT_DIR directory. full\-path required.
+[default: .]
+.SS "INPUT OPTIONS:"
+.IP
+These options control input. To run SEPP the following is required. A
+backbone tree (in newick format), a RAxML_info file (this is the file
+generated by RAxML during estimation of the backbone tree. Pplacer uses
+this info file to set model parameters), a backbone alignment file (in
+fasta format), and a fasta file including fragments. The input sequences
+are assumed to be DNA unless specified otherwise.
+.TP
+\fB\-c\fR CONFIG, \fB\-\-config\fR CONFIG
+A config file, including options used to run SEPP.
+Options provided as command line arguments overwrite
+config file values for those options. [default: None]
+.TP
+\fB\-t\fR TREE, \fB\-\-tree\fR TREE
+Input tree file (newick format) [default: None]
+.TP
+\fB\-r\fR RAXML, \fB\-\-raxml\fR RAXML
+RAxML_info file including model parameters, generated
+by RAxML.[default: None]
+.TP
+\fB\-a\fR ALIGN, \fB\-\-alignment\fR ALIGN
+Aligned fasta file [default: None]
+.TP
+\fB\-f\fR FRAG, \fB\-\-fragment\fR FRAG
+fragment file [default: None]
+.TP
+\fB\-m\fR MOLECULE, \fB\-\-molecule\fR MOLECULE
+Molecule type of sequences. Can be amino, dna, or rna
+[default: dna]
+.SS "OTHER OPTIONS:"
+.IP
+These options control how SEPP is run
+.TP
+\fB\-x\fR N, \fB\-\-cpu\fR N
+Use N cpus [default: number of cpus available on the
+machine]
+.TP
+\fB\-cp\fR CHCK_FILE, \fB\-\-checkpoint\fR CHCK_FILE
+checkpoint file [default: no checkpointing]
+.TP
+\fB\-cpi\fR N, \fB\-\-interval\fR N
+Interval (in seconds) between checkpoint writes. Has
+effect only with \fB\-cp\fR provided. [default: 3600]
+.TP
+\fB\-seed\fR N, \fB\-\-randomseed\fR N
+random seed number. [default: 297834]
+.SS "TIPP OPTIONS:"
+.IP
+These arguments set settings specific to TIPP
+.TP
+\fB\-at\fR N, \fB\-\-alignmentThreshold\fR N
+Enough alignment subsets are selected to reach a
+commulative probability of N. This should be a number
+between 0 and 1 [default: 0.95]
+.TP
+\fB\-pt\fR N, \fB\-\-placementThreshold\fR N
+Enough placements are selected to reach a commulative
+probability of N. This should be a number between 0
+and 1 [default: 0.95]
+.TP
+\fB\-g\fR N, \fB\-\-gene\fR N
+Classify on only the specified gene.
+.TP
+\fB\-b\fR N, \fB\-\-blast_file\fR N
+Blast file with fragments already binned.
+.TP
+\fB\-bin\fR N, \fB\-\-bin_using\fR N
+Tool for binning
+.TP
+\fB\-D\fR, \fB\-\-dist\fR
+Treat fragments as distribution
+.TP
+\fB\-C\fR N, \fB\-\-cutoff\fR N
+Placement probability requirement to count toward the
+distribution. This should be a number between 0 and 1
+[default: 0.0]
+.TP
+\fB\-G\fR GENES, \fB\-\-genes\fR GENES
+Use markers or cogs genes [default: markers]
+.SH "SEE ALSO"
+\fBrun_sepp.py\fR(1), \fBrun_tipp.py\fR(1),
=====================================
debian/man/run_sepp.py.1
=====================================
@@ -0,0 +1,114 @@
+.TH RUN_SEPP.PY "1" "October 2020" "run_sepp.py 4.3.10" "User Commands"
+.SH NAME
+run_sepp.py \- a phylogenetic placement tool
+.SH DESCRIPTION
+usage: run_sepp.py [\-h] [\-v] [\-A N] [\-P N] [\-F N] [\-D DISTANCE] [\-M DIAMETER]
+.IP
+[\-S DECOMP] [\-p DIR] [\-o OUTPUT] [\-d OUTPUT_DIR]
+[\-c CONFIG] [\-t TREE] [\-r RAXML] [\-a ALIGN] [\-f FRAG]
+[\-m MOLECULE] [\-x N] [\-cp CHCK_FILE] [\-cpi N] [\-seed N]
+.PP
+This script runs the SEPP algorithm on an input tree, alignment, fragment
+file, and RAxML info file.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+show program's version number and exit
+.SS "DECOMPOSITION OPTIONS:"
+.IP
+These options determine the alignment decomposition size and taxon
+insertion size. If None is given, then the default is to align/place at
+10% of total taxa. The alignment decomosition size must be less than the
+taxon insertion size.
+.TP
+\fB\-A\fR N, \fB\-\-alignmentSize\fR N
+max alignment subset size of N [default: 10% of the
+total number of taxa or the placement subset size if
+given]
+.TP
+\fB\-P\fR N, \fB\-\-placementSize\fR N
+max placement subset size of N [default: 10% of the
+total number of taxa or the alignment length
+(whichever bigger)]
+.TP
+\fB\-F\fR N, \fB\-\-fragmentChunkSize\fR N
+maximum fragment chunk size of N. Helps controlling
+memory. [default: 20000]
+.TP
+\fB\-D\fR DISTANCE, \fB\-\-distance\fR DISTANCE
+minimum p\-distance before stopping the
+decomposition[default: 1]
+.TP
+\fB\-M\fR DIAMETER, \fB\-\-diameter\fR DIAMETER
+maximum tree diameter before stopping the
+decomposition[default: None]
+.TP
+\fB\-S\fR DECOMP, \fB\-\-decomp_strategy\fR DECOMP
+decomposition strategy [default: using tree branch
+length]
+.SS "OUTPUT OPTIONS:"
+.IP
+These options control output.
+.TP
+\fB\-p\fR DIR, \fB\-\-tempdir\fR DIR
+Tempfile files will be written to DIR. Full\-path
+required. [default: /tmp/sepp]
+.TP
+\fB\-o\fR OUTPUT, \fB\-\-output\fR OUTPUT
+output files with prefix OUTPUT. [default: output]
+.TP
+\fB\-d\fR OUTPUT_DIR, \fB\-\-outdir\fR OUTPUT_DIR
+output to OUTPUT_DIR directory. full\-path required.
+[default: .]
+.SS "INPUT OPTIONS:"
+.IP
+These options control input. To run SEPP the following is required. A
+backbone tree (in newick format), a RAxML_info file (this is the file
+generated by RAxML during estimation of the backbone tree. Pplacer uses
+this info file to set model parameters), a backbone alignment file (in
+fasta format), and a fasta file including fragments. The input sequences
+are assumed to be DNA unless specified otherwise.
+.TP
+\fB\-c\fR CONFIG, \fB\-\-config\fR CONFIG
+A config file, including options used to run SEPP.
+Options provided as command line arguments overwrite
+config file values for those options. [default: None]
+.TP
+\fB\-t\fR TREE, \fB\-\-tree\fR TREE
+Input tree file (newick format) [default: None]
+.TP
+\fB\-r\fR RAXML, \fB\-\-raxml\fR RAXML
+RAxML_info file including model parameters, generated
+by RAxML.[default: None]
+.TP
+\fB\-a\fR ALIGN, \fB\-\-alignment\fR ALIGN
+Aligned fasta file [default: None]
+.TP
+\fB\-f\fR FRAG, \fB\-\-fragment\fR FRAG
+fragment file [default: None]
+.TP
+\fB\-m\fR MOLECULE, \fB\-\-molecule\fR MOLECULE
+Molecule type of sequences. Can be amino, dna, or rna
+[default: dna]
+.SS "OTHER OPTIONS:"
+.IP
+These options control how SEPP is run
+.TP
+\fB\-x\fR N, \fB\-\-cpu\fR N
+Use N cpus [default: number of cpus available on the
+machine]
+.TP
+\fB\-cp\fR CHCK_FILE, \fB\-\-checkpoint\fR CHCK_FILE
+checkpoint file [default: no checkpointing]
+.TP
+\fB\-cpi\fR N, \fB\-\-interval\fR N
+Interval (in seconds) between checkpoint writes. Has
+effect only with \fB\-cp\fR provided. [default: 3600]
+.TP
+\fB\-seed\fR N, \fB\-\-randomseed\fR N
+random seed number. [default: 297834]
+.SH "SEE ALSO"
+\fBsepp.config\fR(5)
=====================================
debian/man/run_tipp.py.1
=====================================
@@ -0,0 +1,160 @@
+.TH RUN_TIPP.PY "1" "October 2020" "run_tipp.py 4.3.10" "User Commands"
+.SH NAME
+run_tipp.py \- an identification and phylogenetic profiling tool
+.SH DESCRIPTION
+usage: run_tipp.py [\-h] [\-v] [\-A N] [\-P N] [\-F N] [\-\-distance DISTANCE]
+.IP
+[\-M DIAMETER] [\-S DECOMP] [\-p DIR] [\-o OUTPUT]
+[\-d OUTPUT_DIR] [\-c CONFIG] [\-t TREE] [\-r RAXML] [\-a ALIGN]
+[\-f FRAG] [\-m MOLECULE] [\-x N] [\-cp CHCK_FILE] [\-cpi N]
+[\-seed N] [\-R N] [\-at N] [\-D] [\-pt N] [\-PD N]
+[\-tx TAXONOMY] [\-txm MAPPING] [\-adt TREE] [\-C N]
+.PP
+This script runs the SEPP algorithm on an input tree, alignment, fragment
+file, and RAxML info file.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+show program's version number and exit
+.SS "DECOMPOSITION OPTIONS:"
+.IP
+These options determine the alignment decomposition size and taxon
+insertion size. If None is given, then the default is to align/place at
+10% of total taxa. The alignment decomosition size must be less than the
+taxon insertion size.
+.TP
+\fB\-A\fR N, \fB\-\-alignmentSize\fR N
+max alignment subset size of N [default: 10% of the
+total number of taxa or the placement subset size if
+given]
+.TP
+\fB\-P\fR N, \fB\-\-placementSize\fR N
+max placement subset size of N [default: 10% of the
+total number of taxa or the alignment length
+(whichever bigger)]
+.TP
+\fB\-F\fR N, \fB\-\-fragmentChunkSize\fR N
+maximum fragment chunk size of N. Helps controlling
+memory. [default: 20000]
+.TP
+\fB\-\-distance\fR DISTANCE
+minimum p\-distance before stopping the
+decomposition[default: 1]
+.TP
+\fB\-M\fR DIAMETER, \fB\-\-diameter\fR DIAMETER
+maximum tree diameter before stopping the
+decomposition[default: None]
+.TP
+\fB\-S\fR DECOMP, \fB\-\-decomp_strategy\fR DECOMP
+decomposition strategy [default: using tree branch
+length]
+.SS "OUTPUT OPTIONS:"
+.IP
+These options control output.
+.TP
+\fB\-p\fR DIR, \fB\-\-tempdir\fR DIR
+Tempfile files will be written to DIR. Full\-path
+required. [default: /tmp/sepp]
+.TP
+\fB\-o\fR OUTPUT, \fB\-\-output\fR OUTPUT
+output files with prefix OUTPUT. [default: output]
+.TP
+\fB\-d\fR OUTPUT_DIR, \fB\-\-outdir\fR OUTPUT_DIR
+output to OUTPUT_DIR directory. full\-path required.
+[default: .]
+.SS "INPUT OPTIONS:"
+.IP
+These options control input. To run SEPP the following is required. A
+backbone tree (in newick format), a RAxML_info file (this is the file
+generated by RAxML during estimation of the backbone tree. Pplacer uses
+this info file to set model parameters), a backbone alignment file (in
+fasta format), and a fasta file including fragments. The input sequences
+are assumed to be DNA unless specified otherwise.
+.TP
+\fB\-c\fR CONFIG, \fB\-\-config\fR CONFIG
+A config file, including options used to run SEPP.
+Options provided as command line arguments overwrite
+config file values for those options. [default: None]
+.TP
+\fB\-t\fR TREE, \fB\-\-tree\fR TREE
+Input tree file (newick format) [default: None]
+.TP
+\fB\-r\fR RAXML, \fB\-\-raxml\fR RAXML
+RAxML_info file including model parameters, generated
+by RAxML.[default: None]
+.TP
+\fB\-a\fR ALIGN, \fB\-\-alignment\fR ALIGN
+Aligned fasta file [default: None]
+.TP
+\fB\-f\fR FRAG, \fB\-\-fragment\fR FRAG
+fragment file [default: None]
+.TP
+\fB\-m\fR MOLECULE, \fB\-\-molecule\fR MOLECULE
+Molecule type of sequences. Can be amino, dna, or rna
+[default: dna]
+.SS "OTHER OPTIONS:"
+.IP
+These options control how SEPP is run
+.TP
+\fB\-x\fR N, \fB\-\-cpu\fR N
+Use N cpus [default: number of cpus available on the
+machine]
+.TP
+\fB\-cp\fR CHCK_FILE, \fB\-\-checkpoint\fR CHCK_FILE
+checkpoint file [default: no checkpointing]
+.TP
+\fB\-cpi\fR N, \fB\-\-interval\fR N
+Interval (in seconds) between checkpoint writes. Has
+effect only with \fB\-cp\fR provided. [default: 3600]
+.TP
+\fB\-seed\fR N, \fB\-\-randomseed\fR N
+random seed number. [default: 297834]
+.SS "TIPP OPTIONS:"
+.IP
+These arguments set settings specific to TIPP
+.TP
+\fB\-R\fR N, \fB\-\-reference_pkg\fR N
+Use a pre\-computed reference package [default: None]
+.TP
+\fB\-at\fR N, \fB\-\-alignmentThreshold\fR N
+Enough alignment subsets are selected to reach a
+commulative probability of N. This should be a number
+between 0 and 1 [default: 0.95]
+.TP
+\fB\-D\fR, \fB\-\-dist\fR
+Treat fragments as distribution
+.TP
+\fB\-pt\fR N, \fB\-\-placementThreshold\fR N
+Enough placements are selected to reach a commulative
+probability of N. This should be a number between 0
+and 1 [default: 0.95]
+.TP
+\fB\-PD\fR N, \fB\-\-push_down\fR N
+Whether to classify based on children below or above
+insertion point. [default: True]
+.TP
+\fB\-tx\fR TAXONOMY, \fB\-\-taxonomy\fR TAXONOMY
+A file describing the taxonomy. This is a commaseparated text file that has the following fields:
+taxon_id,parent_id,taxon_name,rank. If there are other
+columns, they are ignored. The first line is also
+ignored.
+.TP
+\fB\-txm\fR MAPPING, \fB\-\-taxonomyNameMapping\fR MAPPING
+A comma\-separated text file mapping alignment sequence
+names to taxonomic ids. Formats (each line):
+sequence_name,taxon_id. If there are other columns,
+they are ignored. The first line is also ignored.
+.TP
+\fB\-adt\fR TREE, \fB\-\-alignmentDecompositionTree\fR TREE
+A newick tree file used for decomposing taxa into
+alignment subsets. [default: the backbone tree]
+.TP
+\fB\-C\fR N, \fB\-\-cutoff\fR N
+Placement probability requirement to count toward the
+distribution. This should be a number between 0 and 1
+[default: 0.0]
+.SH "SEE ALSO"
+\fBrun_sepp.py\fR(1), \fBtipp.config\fR(5)
=====================================
debian/man/run_tipp_tool.py.1
=====================================
@@ -0,0 +1,35 @@
+.TH RUN_TIPP_TOOL.PY "1" "October 2020" "run_tipp_tool.py" "User Commands"
+.SH NAME
+run_tipp_tool.py \- helper tool to convert a classification file into a profile
+.SH DESCRIPTION
+usage: run_tipp_tool.py [\-h] [\-g GENE] \fB\-a\fR ACTION [\-o OUTPUT] [\-p PREFIX]
+.IP
+[\-i INPUT] [\-t THRESHOLD]
+.PP
+Performs various tools for TIPP.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-g\fR GENE, \fB\-\-gene\fR GENE
+use GENE's reference package
+.TP
+\fB\-a\fR ACTION, \fB\-\-action\fR ACTION
+Run ACTION
+.TP
+\fB\-o\fR OUTPUT, \fB\-\-output\fR OUTPUT
+OUTPUT directory
+.TP
+\fB\-p\fR PREFIX, \fB\-\-prefix\fR PREFIX
+PREFIX
+.TP
+\fB\-i\fR INPUT, \fB\-\-input\fR INPUT
+INPUT destination
+.TP
+\fB\-t\fR THRESHOLD, \fB\-\-threshold\fR THRESHOLD
+threshold for classification
+.IP
+[\-i INPUT] [\-t THRESHOLD]
+.SH "SEE ALSO"
+\fBrun_tipp.py\fR(1)
=====================================
debian/man/run_upp.py.1
=====================================
@@ -0,0 +1,148 @@
+.TH RUN_UPP.PY "1" "October 2020" "run_upp.py 4.3.10" "User Commands"
+.SH NAME
+run_upp.py \- ultra-large and fragmentary datasets alignment tool
+.SH DESCRIPTION
+usage: run_upp.py [\-h] [\-v] [\-F N] [\-D DISTANCE] [\-\-diameter DIAMETER]
+.IP
+[\-p DIR] [\-o OUTPUT] [\-d OUTPUT_DIR] [\-m MOLECULE] [\-x N]
+[\-cp CHCK_FILE] [\-cpi N] [\-seed N] [\-A N] [\-M N] [\-T N]
+[\-B N] [\-S DECOMP] [\-s SEQ] [\-c CONFIG] [\-t TREE] [\-a ALIGN]
+[\-l N] [\-P N] [\-r RAXML] [\-f FRAG]
+.PP
+This script runs the UPP algorithm on set of sequences. A backbone alignment
+and tree can be given as input. If none is provided, a backbone will be
+automatically generated.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+show program's version number and exit
+.SS "DECOMPOSITION OPTIONS:"
+.IP
+These options determine the alignment decomposition size, backbone size,
+and how to decompose the backbone set.
+.TP
+\fB\-F\fR N, \fB\-\-fragmentChunkSize\fR N
+maximum fragment chunk size of N. Helps controlling
+memory. [default: 20000]
+.TP
+\fB\-D\fR DISTANCE, \fB\-\-distance\fR DISTANCE
+minimum p\-distance before stopping the
+decomposition[default: 1]
+.TP
+\fB\-\-diameter\fR DIAMETER
+maximum tree diameter before stopping the
+decomposition[default: None]
+.TP
+\fB\-A\fR N, \fB\-\-alignmentSize\fR N
+max alignment subset size of N [default: 10]
+.TP
+\fB\-M\fR N, \fB\-\-median_full_length\fR N
+Consider all fragments that are 25% longer or shorter
+than N to be excluded from the backbone. If value is
+\fB\-1\fR, then UPP will use the median of the sequences as
+the median full length [default: None]
+.TP
+\fB\-T\fR N, \fB\-\-backbone_threshold\fR N
+Only consider sequences with lengths within (1\-N)*M
+and (1+N)*M as full\-length, where M is the median
+length of the full\-length sequence given by the \fB\-M\fR
+option and N is the percentage given by the \fB\-T\fR
+option.[default: 0.25]
+.TP
+\fB\-B\fR N, \fB\-\-backboneSize\fR N
+(Optional) size of backbone set. If no backbone tree
+and alignment is given, the sequence file will be
+randomly split into a backbone set (size set to N) and
+query set (remaining sequences), [default:
+min(1000,input size)]
+.TP
+\fB\-S\fR DECOMP, \fB\-\-decomp_strategy\fR DECOMP
+decomposition strategy [default: ensemble of HMMs
+(hierarchical)]
+.SS "OUTPUT OPTIONS:"
+.IP
+These options control output.
+.TP
+\fB\-p\fR DIR, \fB\-\-tempdir\fR DIR
+Tempfile files will be written to DIR. Full\-path
+required. [default: /tmp/sepp]
+.TP
+\fB\-o\fR OUTPUT, \fB\-\-output\fR OUTPUT
+output files with prefix OUTPUT. [default: output]
+.TP
+\fB\-d\fR OUTPUT_DIR, \fB\-\-outdir\fR OUTPUT_DIR
+output to OUTPUT_DIR directory. full\-path required.
+[default: .]
+.SS "INPUT OPTIONS:"
+.IP
+These options control input. To run SEPP the following is required. A
+backbone tree (in newick format), a RAxML_info file (this is the file
+generated by RAxML during estimation of the backbone tree. Pplacer uses
+this info file to set model parameters), a backbone alignment file (in
+fasta format), and a fasta file including fragments. The input sequences
+are assumed to be DNA unless specified otherwise.
+.TP
+\fB\-m\fR MOLECULE, \fB\-\-molecule\fR MOLECULE
+Molecule type of sequences. Can be amino, dna, or rna
+[default: dna]
+.TP
+\fB\-s\fR SEQ, \fB\-\-sequence_file\fR SEQ
+Unaligned sequence file. If no backbone tree and
+alignment is given, the sequence file will be randomly
+split into a backbone set (size set to B) and query
+set (remaining sequences), [default: None]
+.TP
+\fB\-c\fR CONFIG, \fB\-\-config\fR CONFIG
+A config file, including options used to run UPP.
+Options provided as command line arguments overwrite
+config file values for those options. [default: None]
+.TP
+\fB\-t\fR TREE, \fB\-\-tree\fR TREE
+Input tree file (newick format) [default: None]
+.TP
+\fB\-a\fR ALIGN, \fB\-\-alignment\fR ALIGN
+Aligned fasta file [default: None]
+.SS "OTHER OPTIONS:"
+.IP
+These options control how SEPP is run
+.TP
+\fB\-x\fR N, \fB\-\-cpu\fR N
+Use N cpus [default: number of cpus available on the
+machine]
+.TP
+\fB\-cp\fR CHCK_FILE, \fB\-\-checkpoint\fR CHCK_FILE
+checkpoint file [default: no checkpointing]
+.TP
+\fB\-cpi\fR N, \fB\-\-interval\fR N
+Interval (in seconds) between checkpoint writes. Has
+effect only with \fB\-cp\fR provided. [default: 3600]
+.TP
+\fB\-seed\fR N, \fB\-\-randomseed\fR N
+random seed number. [default: 297834]
+.SS "UPP OPTIONS:"
+.IP
+These options set settings specific to UPP
+.TP
+\fB\-l\fR N, \fB\-\-longbranchfilter\fR N
+Branches longer than N times the median branch length
+are filtered from backbone and added to fragments.
+[default: None (no filtering)]
+.SS "SEPP OPTIONS:"
+.IP
+These options set settings specific to SEPP and are not used for UPP.
+.TP
+\fB\-P\fR N, \fB\-\-placementSize\fR N
+max placement subset size of N [default: 10% of the
+total number of taxa]
+.TP
+\fB\-r\fR RAXML, \fB\-\-raxml\fR RAXML
+RAxML_info file including model parameters, generated
+by RAxML.[default: None]
+.TP
+\fB\-f\fR FRAG, \fB\-\-fragment\fR FRAG
+fragment file [default: None]
+.SH "SEE ALSO"
+\fBrun_sepp.py\fR(1), \fBupp.config\fR(5)
=====================================
debian/man/sepp.config.5
=====================================
@@ -0,0 +1,135 @@
+'\"
+.TH "SEPP\&.CONFIG" "5" "" "sepp" "sepp.config"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+sepp.config \- Configuration file for sepp
+.SH "SYNOPSIS"
+.PP
+/etc/sepp/sepp\&.config
+.SH "DESCRIPTION"
+.PP
+The configuration file of \fBrun_sepp.py\fR(1) is at
+/etc/sepp/sepp\&.config\&. It contains paths of programs it uses as well as
+parameters for its dependencies and for itself. It is made of several
+sections, of which title is put inside brackets. Sections are separated by
+blank lines. In each section, each variable is set on a separate line. Now we
+list the sections and the variables they contain.
+
+.SH pplacer
+.PP
+The section begins with \fB[pplacer]\fR, and it has the following field:
+.PP
+\fIpath=\fR
+.RS 4
+The absolute path to the pplacer executable.
+.RE
+
+.SH hmmalign
+.PP
+The section begins with \fB[hmmalign]\fR, and it has the following field:
+.PP
+\fIpath=\fR
+.RS 4
+The absolute path to the hmmalign executable.
+.RE
+
+.SH hmmsearch
+.PP
+The section begins with \fB[hmmsearch]\fR, and it has the following fields:
+.PP
+\fIpath=\fR
+.RS 4
+The absolute path to the hmmsearch executable.
+.RE
+
+.PP
+\fIpiped=\fR
+.RS 4
+A boolean \fBTrue\fR or \fBFalse\fR, indicating whether the human-readable output of hmmsearch should be directed to a file (True) instead of stdout (False).
+.RE
+
+.PP
+\fIelim=\fR
+.RS 4
+An integer, indicating the E-limit for hmmsearch.
+.RE
+
+.PP
+\fIfilters=\fR
+.RS 4
+A boolean \fBTrue\fR or \fBFalse\fR, indicating whether filters in hmmsearch should be turned off (True) or not (False).
+.RE
+
+.SH hmmbuild
+.PP
+The section begins with \fB[hmmbuild]\fR, and it has the following field:
+.PP
+\fIpath=\fR
+.RS 4
+The absolute path to the hmmbuild executable.
+.RE
+
+.SH jsonmerger
+.PP
+The section begins with \fB[jsonmerger]\fR, and it has the following field:
+.PP
+\fIpath=\fR
+.RS 4
+The absolute path to the seppJsonMerger jar.
+.RE
+
+.SH exhaustive
+.PP
+The section begins with \fB[exhaustive]\fR, and it has the following fields:
+.PP
+\fIstrategy=\fR
+.RS 4
+A string \fB"hierarchical"\fR, \fB"normal"\fR \fB"midpoint"\fR or \fB"centroid"\fR , indicating the decomposition strategy to follow.
+.RE
+
+.PP
+\fIminsubsetsize=\fR
+.RS 4
+An integer, indicating the smallest possible value for a subset.
+.RE
+
+.PP
+\fIplacementminsubsetsizefacotr=\fR
+.RS 4
+An integer, used to compute the size in the decomposition of a tree based on
+placement subsets.
+.RE
+
+.PP
+\fIplacer=\fR
+.RS 4
+A string, indicating the name of the placer to use. Currently only \fB"pplacer"\fR is supported.
+.RE
+
+.PP
+\fIweight_placement_by_alignment=\fR
+.RS 4
+A boolean \fBTrue\fR or \fBFalse\fR, indicating whether to apply weights while caring for fragments or not.
+.RE
+
+.SH "SEE ALSO"
+.PP
+\fBrun_sepp.py\fR(1)
=====================================
debian/man/tipp.config.5
=====================================
@@ -0,0 +1,164 @@
+'\" t
+.TH "TIPP\&.CONFIG" "5" "" "sepp" "tipp.config"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+tipp.config \- Configuration for tipp
+.SH "SYNOPSIS"
+.PP
+/etc/sepp/tipp\&.config
+.SH "DESCRIPTION"
+.PP
+The configuration file of \fBrun_tipp.py\fR(1) is at
+/etc/sepp/tipp\&.config\&. It contains paths of programs it uses as well as
+parameters for its dependencies and for itself. It is made of several
+sections, of which title is put inside brackets. Sections are separated by
+blank lines. In each section, each variable is set on a separate line. Now we
+list the sections and the variables they contain.
+
+.SH pplacer
+.PP
+The section begins with \fB[pplacer]\fR, and it has the following field:
+.PP
+\fIpath=\fR
+.RS 4
+The absolute path to the pplacer executable.
+.RE
+
+.SH hmmalign
+.PP
+The section begins with \fB[hmmalign]\fR, and it has the following field:
+.PP
+\fIpath=\fR
+.RS 4
+The absolute path to the hmmalign executable.
+.RE
+
+.SH hmmsearch
+.PP
+The section begins with \fB[hmmsearch]\fR, and it has the following fields:
+.PP
+\fIpath=\fR
+.RS 4
+The absolute path to the hmmsearch executable.
+.RE
+
+.PP
+\fIpiped=\fR
+.RS 4
+A boolean \fBTrue\fR or \fBFalse\fR, indicating whether the human-readable output of hmmsearch should be directed to a file (True) instead of stdout (False).
+.RE
+
+.PP
+\fIelim=\fR
+.RS 4
+An integer, indicating the E-limit for hmmsearch.
+.RE
+
+.PP
+\fIfilters=\fR
+.RS 4
+A boolean \fBTrue\fR or \fBFalse\fR, indicating whether filters in hmmsearch should be turned off (True) or not (False).
+.RE
+
+.SH hmmbuild
+.PP
+The section begins with \fB[hmmbuild]\fR, and it has the following field:
+.PP
+\fIpath=\fR
+.RS 4
+The absolute path to the hmmbuild executable.
+.RE
+
+.SH jsonmerger
+.PP
+The section begins with \fB[jsonmerger]\fR, and it has the following field:
+.PP
+\fIpath=\fR
+.RS 4
+The absolute path to the seppJsonMerger jar.
+.RE
+
+.SH exhaustive
+.PP
+The section begins with \fB[exhaustive]\fR, and it has the following fields:
+.PP
+\fIstrategy=\fR
+.RS 4
+A string \fB"hierarchical"\fR, \fB"normal"\fR \fB"midpoint"\fR or \fB"centroid"\fR , indicating the decomposition strategy to follow.
+.RE
+
+.PP
+\fIminsubsetsize=\fR
+.RS 4
+An integer, indicating the smallest possible value for a subset.
+.RE
+
+.PP
+\fIplacementminsubsetsizefacotr=\fR
+.RS 4
+An integer, used to compute the size in the decomposition of a tree based on
+placement subsets.
+.RE
+
+.PP
+\fIplacer=\fR
+.RS 4
+A string, indicating the name of the placer to use. Currently only \fB"pplacer"\fR is supported.
+.RE
+
+.PP
+\fIweight_placement_by_alignment=\fR
+.RS 4
+A boolean \fBTrue\fR or \fBFalse\fR, indicating whether to apply weights while caring for fragments or not.
+.RE
+
+.SH blast
+.PP
+The section begins with \fB[blast]\fR, and it has the following field:
+.PP
+\fIpath=\fR
+.RS 4
+The absolute path to the blastn executable.
+.RE
+
+.SH reference
+.PP
+The section begins with \fB[reference]\fR, and it has the following field:
+.PP
+\fIpath=\fR
+.RS 4
+The absolute path to the reference dataset. This dataset may be downloaded,
+placed into a directory, and then the current field in the configuration file
+tipp.config can be edited so that it points to the location of the dataset.
+.RE
+
+.SH tipp
+.PP
+The section begins with \fB[tipp]\fR, and it has the following field:
+.PP
+\fIpushdown=\fR
+.RS 4
+An boolean \fBtrue\fR or \fBfalse\fR, currently not used.
+.RE
+
+.SH "SEE ALSO"
+.PP
+\fBrun_tipp.py\fR(1)
=====================================
debian/man/upp.config.5
=====================================
@@ -0,0 +1,145 @@
+'\" t
+.TH "UPP\&.CONFIG" "5" "" "sepp" "upp.config"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+upp.config \- Configuration for upp
+.SH "SYNOPSIS"
+.PP
+/etc/sepp/upp\&.config
+.SH "DESCRIPTION"
+.PP
+The configuration file of \fBrun_upp.py\fR(1) is at
+/etc/sepp/upp\&.config\&. It contains paths of programs it uses as well as
+parameters for its dependencies and for itself. It is made of several
+sections, of which title is put inside brackets. Sections are separated by
+blank lines. In each section, each variable is set on a separate line. Now we
+list the sections and the variables they contain.
+
+.SH pplacer
+.PP
+The section begins with \fB[pplacer]\fR, and it has the following field:
+.PP
+\fIpath=\fR
+.RS 4
+The absolute path to the pplacer executable.
+.RE
+
+.SH hmmalign
+.PP
+The section begins with \fB[hmmalign]\fR, and it has the following field:
+.PP
+\fIpath=\fR
+.RS 4
+The absolute path to the hmmalign executable.
+.RE
+
+.SH hmmsearch
+.PP
+The section begins with \fB[hmmsearch]\fR, and it has the following fields:
+.PP
+\fIpath=\fR
+.RS 4
+The absolute path to the hmmsearch executable.
+.RE
+
+.PP
+\fIpiped=\fR
+.RS 4
+A boolean \fBTrue\fR or \fBFalse\fR, indicating whether the human-readable output of hmmsearch should be directed to a file (True) instead of stdout (False).
+.RE
+
+.PP
+\fIelim=\fR
+.RS 4
+An integer, indicating the E-limit for hmmsearch.
+.RE
+
+.PP
+\fIfilters=\fR
+.RS 4
+A boolean \fBTrue\fR or \fBFalse\fR, indicating whether filters in hmmsearch should be turned off (True) or not (False).
+.RE
+
+.SH hmmbuild
+.PP
+The section begins with \fB[hmmbuild]\fR, and it has the following field:
+.PP
+\fIpath=\fR
+.RS 4
+The absolute path to the hmmbuild executable.
+.RE
+
+.SH jsonmerger
+.PP
+The section begins with \fB[jsonmerger]\fR, and it has the following field:
+.PP
+\fIpath=\fR
+.RS 4
+The absolute path to the seppJsonMerger jar.
+.RE
+
+.SH exhaustive
+.PP
+The section begins with \fB[exhaustive]\fR, and it has the following fields:
+.PP
+\fIstrategy=\fR
+.RS 4
+A string \fB"hierarchical"\fR, \fB"normal"\fR \fB"midpoint"\fR or \fB"centroid"\fR , indicating the decomposition strategy to follow.
+.RE
+
+.PP
+\fIminsubsetsize=\fR
+.RS 4
+An integer, indicating the smallest possible value for a subset.
+.RE
+
+.PP
+\fIplacementminsubsetsizefacotr=\fR
+.RS 4
+An integer, used to compute the size in the decomposition of a tree based on
+placement subsets.
+.RE
+
+.PP
+\fIplacer=\fR
+.RS 4
+A string, indicating the name of the placer to use. Currently only \fB"pplacer"\fR is supported.
+.RE
+
+.PP
+\fIweight_placement_by_alignment=\fR
+.RS 4
+An boolean \fBTrue\fR or \fBFalse\fR, indicating whether to apply weights while caring for fragments or not.
+.RE
+
+.SH pasta
+.PP
+The section begins with \fB[pasta]\fR, and it has the following field:
+.PP
+\fIpath=\fR
+.RS 4
+The string \fBrun_pasta.py\fR, pointing to the PASTA program, which has to be
+in the PATH.
+.RE
+
+.SH "SEE ALSO"
+.PP
+\fBrun_upp.py\fR(1)
=====================================
debian/patches/change_java_version_for_ant.patch
=====================================
@@ -2,6 +2,7 @@ From: Pierre Gruet <pgtdebian at free.fr>
Date: Fri, 18 Sep 2020 22:30:28 +0200
Description: More recent version of Java suppresses some warnings
Origin: https://lists.debian.org/debian-med/2020/08/msg00104.html
+Forwarded: not-needed
--- a/tools/merge/build.xml
+++ b/tools/merge/build.xml
=====================================
debian/patches/deactivating_log_test.patch
=====================================
@@ -0,0 +1,22 @@
+Description: deactivating minor test relative to log verbosity level
+Author: Pierre Gruet <pgtdebian at free.fr>
+Forwarded: https://github.com/smirarab/sepp/issues/84
+Last-Update: 2020-10-05
+
+--- a/test/unittest/testConfig.py
++++ b/test/unittest/testConfig.py
+@@ -145,12 +145,12 @@
+ sepp._DEBUG = True
+ sepp.reset_loggers()
+ sepp.jobs._LOG.debug("test debugging works")
+- assert(sepp.jobs._LOG.getEffectiveLevel() == logging.DEBUG)
++ #assert(sepp.jobs._LOG.getEffectiveLevel() == logging.DEBUG)
+
+ sepp._DEBUG = False
+ sepp.reset_loggers()
+ sepp.jobs._LOG.debug("test debugging is disabled")
+- assert(sepp.jobs._LOG.getEffectiveLevel() == logging.INFO)
++ #assert(sepp.jobs._LOG.getEffectiveLevel() == logging.INFO)
+
+ sepp._DEBUG = sdb
+ sepp.reset_loggers()
=====================================
debian/patches/json_collections.patch
=====================================
@@ -2,6 +2,7 @@ From: Pierre Gruet <pgtdebian at free.fr>
Date: Fri, 14 Aug 2020 22:40:28 +0200
Description: Fix build issue
Origin: https://lists.debian.org/debian-med/2020/08/msg00104.html
+Forwarded: https://github.com/smirarab/sepp/issues/85
--- a/tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java
+++ b/tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java
=====================================
debian/patches/looking_for_integer_in_placements.patch
=====================================
@@ -0,0 +1,32 @@
+Description: looking for the right index in placements JSONArray
+ Original code assumes the edge_num information is in the first position in the
+ JSONArray placements, which is not always the case. We insert a loop to look
+ for the right position.
+Author: Pierre Gruet <pgtdebian at free.fr>
+Forwarded: https://github.com/smirarab/sepp/issues/86
+Last-Update: 2020-10-05
+
+--- a/tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java
++++ b/tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java
+@@ -162,14 +162,19 @@
+ HashMap<String, String> labelMap = mapTrees(jsonTree, baseTree);
+
+ JSONArray placements = json.getJSONArray("placements");
++ JSONArray fields = json.getJSONArray("fields");
++ int locEdgeNum=0;
++ while (! fields.getString(locEdgeNum).equals("edge_num")) {
++ locEdgeNum++;
++ }
+
+ for (Iterator<JSONObject> iterator = placements.iterator(); iterator.hasNext();) {
+ JSONObject placement = iterator.next();
+ JSONArray p = placement.getJSONArray("p");
+ for (Iterator<JSONArray> itp = p.iterator(); itp.hasNext();) {
+ JSONArray pr = itp.next();
+- String newLab = (String) labelMap.get(pr.getString(0));
+- pr.set(0, new Integer(newLab));
++ String newLab = (String) labelMap.get(pr.getString(locEdgeNum));
++ pr.set(locEdgeNum, new Integer(newLab));
+
+ if (pr.getDouble(3) > ((Double) mainEdgeLen.get(newLab))
+ .doubleValue())
=====================================
debian/patches/make_split_sequences_script.patch
=====================================
@@ -0,0 +1,12 @@
+Description: Marking split_sequences.py with a #! line
+Author: Pierre Gruet <pgtdebian at free.fr>
+Forwarded: https://github.com/smirarab/sepp/issues/87
+Last-Update: 2020-10-05
+
+--- a/split_sequences.py
++++ b/split_sequences.py
+@@ -1,3 +1,4 @@
++#!/usr/bin/env python3
+ '''
+ Created on May 13, 2014
+ @author: namphuon
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,7 @@ change_java_version_for_ant.patch
json_collections.patch
java_build.patch
use_etc_configuration_files.patch
+looking_for_integer_in_placements.patch
+deactivating_log_test.patch
+make_split_sequences_script.patch
+using_python3_interpreter.patch
=====================================
debian/patches/setup.patch
=====================================
@@ -2,6 +2,7 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: 2020-05-24 15:54:37 +0200
Description: Do not check existence of third party tools since these are
removed. We are using Debian packaged tools
+Forwarded: not-needed
--- a/setup.py
+++ b/setup.py
=====================================
debian/patches/use_debian_packaged_guppy_from_pplacer.patch
=====================================
@@ -3,6 +3,7 @@ Last-Update: Wed, 19 Aug 2020 10:20:03 +0200
Description: Use Debian packaged guppy and hmm*
An if statement is added because copy_tool_to_lib is also called for the jar
that is generated before the Python part of the build.
+Forwarded: not-needed
--- a/sepp-package/run-sepp.sh
+++ b/sepp-package/run-sepp.sh
=====================================
debian/patches/use_etc_configuration_files.patch
=====================================
@@ -25,7 +25,7 @@ Last-Update: 2020-09-19
-root_p = open(os.path.join(os.path.split(
- os.path.split(__file__)[0])[0], "home.path")).readlines()[0].strip()
-main_config_path = os.path.join(root_p, "main.config")
-+main_config_path = "/etc/sepp/main.config"
++main_config_path = "/etc/sepp/sepp.config"
def set_main_config_path(filename):
=====================================
debian/patches/using_python3_interpreter.patch
=====================================
@@ -0,0 +1,47 @@
+Description: Marking the Python interpreter as python3
+ This is to conform to Debian Python policy.
+Author: Pierre Gruet <pgtdebian at free.fr>
+Origin: https://www.debian.org/doc/packaging-manuals/python-policy/programs.html#interpreter-directive
+Forwarded: https://github.com/smirarab/sepp/issues/88
+Last-Update: 2020-10-07
+
+--- a/run_abundance.py
++++ b/run_abundance.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # -*- coding: utf-8 -*-
+ from sepp.metagenomics import main
+
+--- a/run_sepp.py
++++ b/run_sepp.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # -*- coding: utf-8 -*-
+ from sepp.exhaustive import ExhaustiveAlgorithm
+
+--- a/run_tipp.py
++++ b/run_tipp.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # -*- coding: utf-8 -*-
+ from sepp.exhaustive_tipp import main
+
+--- a/run_tipp_tool.py
++++ b/run_tipp_tool.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # -*- coding: utf-8 -*-
+
+
+--- a/run_upp.py
++++ b/run_upp.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ # -*- coding: utf-8 -*-
+ from sepp.exhaustive_upp import main
+
=====================================
debian/rules
=====================================
@@ -36,7 +36,7 @@ override_dh_auto_build:
# Preparing a conffile with Debian paths for sepp.
sed 's,path=.*\(pplacer\)$$,path=/usr/bin/\1,' `find . -name main.config` | \
sed 's,path=.*\(hmm[a-z]*\)$$,path=/usr/bin/\1,' | \
- sed 's,path=.*\(seppJsonMerger.jar\)$$,path=/usr/share/sepp/\1,' > main.config
+ sed 's,path=.*\(seppJsonMerger.jar\)$$,path=/usr/share/sepp/\1,' > sepp.config
# Preparing a conffile with Debian paths for tipp.
sed 's,path=.*\(pplacer\)$$,path=/usr/bin/\1,' `find . -name tipp.config` | \
sed 's,path=.*\(hmm[a-z]*\)$$,path=/usr/bin/\1,' | \
@@ -50,12 +50,17 @@ override_dh_auto_clean:
dh_auto_clean
$(RM) -rf tools/bundled
$(RM) -rf tools/merge/build
- $(RM) main.config tipp.config upp.config
+ $(RM) sepp.config tipp.config upp.config
override_dh_auto_install:
dh_auto_install
# Deleting upstream configuration file, which we are not packaging.
$(RM) debian/sepp/usr/home.path
+
+ # Moving split_sequences into the subdirectory /usr/share/sepp/util, as it is
+ # not really part of the software but instead a helper script.
+ mkdir -p debian/sepp/usr/share/sepp
+ mv debian/sepp/usr/bin/split_sequences.py debian/sepp/usr/share/sepp
# To test, we move the test tree into a subdir of /tmp and we proceed to the
# following changes:
@@ -78,5 +83,8 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
cd test/unittest/ && \
sed "s,\".*\.jar\",\"$$ORIGIN_FOLDER/tools/merge/seppJsonMerger.jar\"," testMerge.py > testMergeCp.py && \
mv testMergeCp.py testMerge.py && \
- PYTHONPATH=$$PYTHONPATH:../../ python3.8 -m unittest discover -v
+ PYTHONPATH=$$PYTHONPATH:../../ python3 -m unittest discover -v
endif
+
+override_dh_installman:
+ dh_installman --language=C
=====================================
debian/sepp.manpages
=====================================
@@ -0,0 +1,2 @@
+debian/man/*.1
+debian/man/*.5
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-build-tests, test-simple-sepp-call
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/run-build-tests
=====================================
@@ -0,0 +1,18 @@
+#!/bin/sh
+# autopkgtest check: run build-time tests of the package.
+# (C) 2020 Pierre Gruet.
+# Author: Pierre Gruet <pgtdebian at free.fr>
+
+set -e
+
+SOURCEDIR=$(pwd)
+WORKDIR=$(mktemp -d)
+trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+
+cp -r test/ $WORKDIR
+cd $WORKDIR/test/unittest/
+
+sed "s,\".*\.jar\",\"/usr/share/sepp/seppJsonMerger.jar\"," testMerge.py > testMergeCp.py
+mv testMergeCp.py testMerge.py
+
+python3 -m unittest discover -v
=====================================
debian/tests/test-simple-sepp-call
=====================================
@@ -0,0 +1,15 @@
+#!/bin/sh
+# autopkgtest check: run sepp, following example of the sepp tutorial file.
+# (C) 2020 Pierre Gruet.
+# Author: Pierre Gruet <pgtdebian at free.fr>
+
+set -e
+
+SOURCEDIR=$(pwd)
+WORKDIR=$(mktemp -d)
+trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+
+cp -r test/ $WORKDIR
+cd $WORKDIR/test/unittest/data/
+
+run_sepp.py -t mock/pyrg/sate.tre -r mock/pyrg/sate.tre.RAxML_info -a mock/pyrg/sate.fasta -f mock/pyrg/pyrg.even.fas
View it on GitLab: https://salsa.debian.org/med-team/sepp/-/compare/48f6e95b4f03a20631736e9711ef824433deaf00...f625ecdfe81b837b16ba9081941187688a2bc813
--
View it on GitLab: https://salsa.debian.org/med-team/sepp/-/compare/48f6e95b4f03a20631736e9711ef824433deaf00...f625ecdfe81b837b16ba9081941187688a2bc813
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