[med-svn] [Git][med-team/sepp][master] 4 commits: Merging d/sepp.install and d/install

[Pierre Gruet]

Pierre Gruet pushed to branch master at Debian Med / sepp


Commits:
7b9a2165 by Pierre Gruet at 2020-12-24T15:12:22+01:00
Merging d/sepp.install and d/install

d/install was ignored due to d/sepp.install being added

- - - - -
e408815a by Pierre Gruet at 2020-12-24T16:11:05+01:00
Adding manpage for run-sepp.sh

- - - - -
c8bb04ab by Pierre Gruet at 2020-12-24T16:11:25+01:00
Fixing typo in d/u/metadata

- - - - -
4efac1b0 by Pierre Gruet at 2020-12-24T16:38:32+01:00
Upload to unstable

- - - - -


6 changed files:

- debian/changelog
- − debian/install
- + debian/man/run-sepp.sh.1
- debian/sepp.install
- debian/sepp.manpages
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+sepp (4.3.10+dfsg-5) unstable; urgency=medium
+
+  * Merging d/sepp.install and d/install
+  * Adding manpage for run-sepp.sh
+  * Fixing typo in d/u/metadata
+
+ -- Pierre Gruet <pgtdebian at free.fr>  Thu, 24 Dec 2020 16:11:31 +0100
+
 sepp (4.3.10+dfsg-4) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/install deleted
=====================================
@@ -1,4 +0,0 @@
-sepp.config etc/sepp
-tipp.config etc/sepp
-# upp.config etc/sepp
-tools/merge/*JsonMerger.jar usr/share/sepp/


=====================================
debian/man/run-sepp.sh.1
=====================================
@@ -0,0 +1,41 @@
+.TH RUN-SEPP.SH "1" "December 2020" "run-sepp.sh 4.3.10" "User Commands"
+.SH NAME
+run-sepp.sh \- a phylogenetic placement tool
+.SH DESCRIPTION
+usage: run\-sepp.sh [input fragments file] [output prefix] [\fB\-x\fR N] [\fB\-A\fR ALIGN] [\fB\-P\fR N] [any other SEPP argument] [\fB\-t\fR TREE] [\fB\-a\fR ALIGN] [\fB\-r\fR RAXML] [\fB\-n\fR argN] [\fB\-b\fR argB]
+.SS "OPTIONS"
+.TP
+\fB\-x\fR N, \fB\-\-cpu N\fR
+Use N cpus [default: number of cpus available on the machine]
+.TP
+\fB\-A\fR ALIGN, \fB\-\-alignmentSize\fR ALIGN
+max alignment subset size of ALIGN [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\-t\fR TREE, \fB\-\-referencePhylogeny\fR TREE
+Input tree file (newick format) [default: None]
+.TP
+\fB\-a\fR ALIGN, \fB\-\-referenceAlignment\fR ALIGN
+Aligned fasta file [default: None]
+.TP
+\fB\-r\fR RAXML, \fB\-\-referenceInfoFile\fR RAXML
+RAxML_info file including model parameters, generated
+by RAxML.[default: None]
+.TP
+\fB\-n\fR argN, \fB\-\-noTreeComputation\fR argN
+if set to something (for instance 1), no tree computation is made, just the placements one.
+.TP
+\fB\-b\fR argB, \fB\-\-debugInformation\fR argB
+If set to something (for instance 1), report debugging information.
+.IP
+Optional commands need not be in order. Any SEPP option can also be passed. For example, use
+\fB\-x\fR 8
+to make SEPP us 8 threads
+.SH "SEE ALSO"
+\fBrun_sepp.py\fR(5)


=====================================
debian/sepp.install
=====================================
@@ -1 +1,5 @@
 sepp-package/run-sepp.sh	usr/bin
+sepp.config etc/sepp
+tipp.config etc/sepp
+# upp.config etc/sepp
+tools/merge/*JsonMerger.jar usr/share/sepp/


=====================================
debian/sepp.manpages
=====================================
@@ -1,4 +1,5 @@
 debian/man/run_abundance.py.1
+debian/man/run-sepp.sh.1
 debian/man/run_sepp.py.1
 debian/man/run_tipp.py.1
 debian/man/run_tipp_tool.py.1


=====================================
debian/upstream/metadata
=====================================
@@ -3,7 +3,7 @@ Registry:
    Entry: sepp
  - Name: bio.tools
    Entry: NA
- - Name; SciCrunch
+ - Name: SciCrunch
    Entry: NA
 Bug-Database: https://github.com/smirarab/sepp/issues
 Bug-Submit: https://github.com/smirarab/sepp/issues/new



View it on GitLab: https://salsa.debian.org/med-team/sepp/-/compare/5fd4cab3e7c8a096cb4b631b60916b75eddc0503...4efac1b08388d06a5d6c9c4e1936d89ae10872c7

-- 
View it on GitLab: https://salsa.debian.org/med-team/sepp/-/compare/5fd4cab3e7c8a096cb4b631b60916b75eddc0503...4efac1b08388d06a5d6c9c4e1936d89ae10872c7
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