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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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