Hi Emilio
On Wed, Mar 22, 2017 at 06:28:03PM +0100, Emilio Pozuelo Monfort wrote:
> Control: tags -1 confirmed moreinfo
>
> On 22/03/17 12:14, Andreas Tille wrote:
> > Package: release.debian.org
> > Severity: normal
> > User: release.debian....@packages.debian.org
> > Usertags: unblock
> >
> > Please unblock package seer
> >
> > The upload fixes #858430.
> >
> > Question: I followed freeze policy for minimum changes. Usually I'd
> > like to provide manpages for new executables in /usr/bin and I would
> > probably also have patched the usage hint to match the actual script
> > name (usage contains wrong path and .pl extension). Would it be in line
> > with the freeze policy to add this polishing which would add quite some
> > diff that is not totally necessary to fix the bug.
>
> That should be fine. Go ahead.
I've attached a new debdiff including better documentation. When
uploading I realised that upload of seer_1.1.2-2 (see last debdiff) was
somehow lost. So please excuse the missing version seer_1.1.2-2 which
is mentioned in the changelog and see attached debdiff between 1.1.2-1
and 1.1.2-3.
Sorry for the mess and thanks for your patience with the release
Andreas.
PS: I'm going to manually close bug #858430 which was closed in the
changelog paragraph of 1.1.2-2.
--
http://fam-tille.de
diff -Nru seer-1.1.2/debian/changelog seer-1.1.2/debian/changelog
--- seer-1.1.2/debian/changelog 2016-12-07 23:05:02.000000000 +0100
+++ seer-1.1.2/debian/changelog 2017-03-23 14:33:36.000000000 +0100
@@ -1,3 +1,16 @@
+seer (1.1.2-3) unstable; urgency=medium
+
+ * Better documentation of scripts
+
+ -- Andreas Tille <ti...@debian.org> Thu, 23 Mar 2017 14:33:36 +0100
+
+seer (1.1.2-2) unstable; urgency=medium
+
+ * Install all available scripts in scripts/ dir into binary package
+ Closes: #858430
+
+ -- Andreas Tille <ti...@debian.org> Wed, 22 Mar 2017 11:43:16 +0100
+
seer (1.1.2-1) unstable; urgency=medium
* New upstream version
diff -Nru seer-1.1.2/debian/mans/blast_top_hits.1
seer-1.1.2/debian/mans/blast_top_hits.1
--- seer-1.1.2/debian/mans/blast_top_hits.1 2016-12-07 23:05:02.000000000
+0100
+++ seer-1.1.2/debian/mans/blast_top_hits.1 2017-03-23 14:33:36.000000000
+0100
@@ -1,9 +1,8 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
-.TH BLAST_TOP_HITS "1" "March 2016" "blast_top_hits 1.1.0" "User Commands"
+.TH BLAST_TOP_HITS "1" "March 2017" "blast_top_hits 1.1.2" "User Commands"
.SH NAME
blast_top_hits \- reduces a blast or blat output file to the top hit for each
query sequence only
.SH SYNOPSIS
-.B blast_top_hits.pl
+.B blast_top_hits
\fI\,--input blast_out --mode blast <options>\/\fR
.SH DESCRIPTION
Reduces a blast or blat output file to the top hit for each query sequence
only.
diff -Nru seer-1.1.2/debian/mans/combineKmers.1
seer-1.1.2/debian/mans/combineKmers.1
--- seer-1.1.2/debian/mans/combineKmers.1 2016-12-07 23:05:02.000000000
+0100
+++ seer-1.1.2/debian/mans/combineKmers.1 2017-03-23 14:33:36.000000000
+0100
@@ -1,5 +1,4 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
-.TH COMBINEKMERS "1" "March 2016" "combineKmers 1.1.0" "User Commands"
+.TH COMBINEKMERS "1" "March 2017" "combineKmers 1.1.2" "User Commands"
.SH NAME
combineKmers \- basic algorithm to combine kmer counts across samples
.P
diff -Nru seer-1.1.2/debian/mans/filter_seer.1
seer-1.1.2/debian/mans/filter_seer.1
--- seer-1.1.2/debian/mans/filter_seer.1 2016-12-07 23:05:02.000000000
+0100
+++ seer-1.1.2/debian/mans/filter_seer.1 2017-03-23 14:33:36.000000000
+0100
@@ -1,5 +1,4 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
-.TH FILTER_SEER "1" "March 2016" "filter_seer 1.1.0" "User Commands"
+.TH FILTER_SEER "1" "March 2017" "filter_seer 1.1.2" "User Commands"
.SH NAME
filter_seer \- post filtering of significant kmers
.SH DESCRIPTION
diff -Nru seer-1.1.2/debian/mans/hits_to_fastq.1
seer-1.1.2/debian/mans/hits_to_fastq.1
--- seer-1.1.2/debian/mans/hits_to_fastq.1 1970-01-01 01:00:00.000000000
+0100
+++ seer-1.1.2/debian/mans/hits_to_fastq.1 2017-03-23 14:33:36.000000000
+0100
@@ -0,0 +1,22 @@
+.TH HITS_TO_FASTQ "1" "March 2017" "hits_to_fastq 1.1.2" "User Commands"
+.SH NAME
+hits_to_fastq \- create a fastq for mapping from significant kmers
+.SH SYNOPSIS
+.B hits_to_fastq
+\fI\,-k <significant_kmers.txt> -b <bonferroni_correction>\/\fR
+.SH DESCRIPTION
+Creates a fastq for mapping from significant kmers
+.SH OPTIONS
+.SS Required
+.TP
+\fB\-k\fR, \fB\-\-kmers\fR
+Significant kmers, as output by seer
+.TP
+\fB\-b\fR, \fB\-\-bonf\fR
+Bonferroni correction to use (try 10e\-8)
+.SS Optional
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Displays this message
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can
be used for any other usage of the program.
diff -Nru seer-1.1.2/debian/mans/kmds.1 seer-1.1.2/debian/mans/kmds.1
--- seer-1.1.2/debian/mans/kmds.1 2016-12-07 23:05:02.000000000 +0100
+++ seer-1.1.2/debian/mans/kmds.1 2017-03-23 14:33:36.000000000 +0100
@@ -1,5 +1,4 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
-.TH KMDS "1" "March 2016" "kmds 1.1.0" "User Commands"
+.TH KMDS "1" "March 2017" "kmds 1.1.2" "User Commands"
.SH NAME
kmds \- control for population structure
.SH DESCRIPTION
@@ -9,7 +8,7 @@
.SH OPTIONS
1) filter and subsample with \fB\-\-no_mds\fR and \fB\-\-size\fR
.P
-2) combine, and do metric multidimensional scaling with \fB\-\-combine_mds\fR
+2) combine, and do metric multidimensional scaling with \fB\-\-mds_concat\fR
.SS "Required options:"
.TP
\fB\-k\fR [ \fB\-\-kmers\fR ] arg
@@ -54,12 +53,11 @@
.TP
\fB\-\-min_words\fR arg
minimum kmer occurrences. Overrides \fB\-\-maf\fR
-.TP
-\fB\-\-chisq\fR arg (=10e\-5)
-p\-value threshold for initial chi squared test. Set
-to 1 to show all
.SS "Other options:"
.TP
+\fB\-\-version\fR
+prints version and exits
+.TP
\fB\-h\fR [ \fB\-\-help\fR ]
full help message
.SH EXAMPLE
diff -Nru seer-1.1.2/debian/mans/map_back.1 seer-1.1.2/debian/mans/map_back.1
--- seer-1.1.2/debian/mans/map_back.1 2016-12-07 23:05:02.000000000 +0100
+++ seer-1.1.2/debian/mans/map_back.1 2017-03-23 14:33:36.000000000 +0100
@@ -1,5 +1,4 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
-.TH MAP_BACK "1" "March 2016" "map_back 1.1.0" "User Commands"
+.TH MAP_BACK "1" "March 2017" "map_back 1.1.2" "User Commands"
.SH NAME
map_back \- context of significant kmers
.SH DESCRIPTION
@@ -20,6 +19,9 @@
\fB\-\-threads\fR arg (=1)
number of threads. Suggested: 4
.TP
+\fB\-\-version\fR
+prints version and exits
+.TP
\fB\-h\fR [ \fB\-\-help\fR ]
full help message
.SH AUTHOR
diff -Nru seer-1.1.2/debian/mans/mapping_to_phandango.1
seer-1.1.2/debian/mans/mapping_to_phandango.1
--- seer-1.1.2/debian/mans/mapping_to_phandango.1 1970-01-01
01:00:00.000000000 +0100
+++ seer-1.1.2/debian/mans/mapping_to_phandango.1 2017-03-23
14:33:36.000000000 +0100
@@ -0,0 +1,25 @@
+.TH MAPPING_TO_PHANDANGO "1" "March 2017" "mapping_to_phandango 1.1.2" "User
Commands"
+.SH NAME
+mapping_to_phandango \- create a plot file for visualisation in phandango
+.SH SYNOPSIS
+.B mapping_to_phandango
+\fI\,-s <sam_file> -k <seer_kmers> > phandango.plot\/\fR
+.SH DESCRIPTION
+Creates a plot file for visualisation in phandango
+.SH OPTIONS
+.SS Required
+.TP
+\fB\-s\fR, \fB\-\-sam\fR
+Sam file of kmers mapped to reference (unsorted)
+.TP
+\fB\-k\fR, \fB\-\-kmers\fR
+Kmers that were mapped
+.SS Optional
+.TP
+\fB\-m\fR, \fB\-\-map\fR
+Minimum mapping quality
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Displays this message
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can
be used for any other usage of the program.
diff -Nru seer-1.1.2/debian/mans/mash2matrix.1
seer-1.1.2/debian/mans/mash2matrix.1
--- seer-1.1.2/debian/mans/mash2matrix.1 1970-01-01 01:00:00.000000000
+0100
+++ seer-1.1.2/debian/mans/mash2matrix.1 2017-03-23 14:33:36.000000000
+0100
@@ -0,0 +1,26 @@
+.TH MASH2MATRIX "1" "March 2017" "mash2matrix 1.1.2" "User Commands"
+.SH NAME
+mash2matrix \- create all pairwise distances between samples
+.SH SYNOPSIS
+.B mash2matrix
+\fI\,<matrix_in> > all_distances.csv\/\fR
+.SH DESCRIPTION
+Uses mash (http://mash.readthedocs.io/) to create all pairwise distances
+between samples.
+.PP
+NB: the input to mash should be the same order as the .pheno file
+generate <assemblies.fa> with:
+.IP
+cut \fB\-f\fR 1 metadata.pheno | tr '
+
+\&' ' '
+.PP
+Then run
+.IP
+mash sketch \fB\-o\fR reference <assemblies.fa>
+.IP
+mash dist reference.msh reference.msh > mash_distances.txt
+.IP
+mash2matrix mash_distances.txt > all_distances.csv
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can
be used for any other usage of the program.
diff -Nru seer-1.1.2/debian/mans/reformat_output.1
seer-1.1.2/debian/mans/reformat_output.1
--- seer-1.1.2/debian/mans/reformat_output.1 1970-01-01 01:00:00.000000000
+0100
+++ seer-1.1.2/debian/mans/reformat_output.1 2017-03-23 14:33:36.000000000
+0100
@@ -0,0 +1,22 @@
+.TH REFORMAT_OUTPUT "1" "March 2017" "reformat_output 1.1.2" "User Commands"
+.SH NAME
+reformat_output \- reformats output for easier reading as tsv
+.SH SYNOPSIS
+.B hits_to_matrix.pl
+\fI\,-k <filtered_kmers.txt> -p <pheno_file>\/\fR
+.SH DESCRIPTION
+Reformats output for easier reading as tsv. Prints to stdout
+.SH OPTIONS
+.SS Required
+.TP
+\fB\-k\fR, \fB\-\-kmers\fR
+Filtered significant kmers, as output by seer + filter_seer
+.TP
+\fB\-p\fR, \fB\-\-pheno\fR
+Phenotype file used by seer
+.SS Optional
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Displays this message
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can
be used for any other usage of the program.
diff -Nru seer-1.1.2/debian/mans/R_mds.1 seer-1.1.2/debian/mans/R_mds.1
--- seer-1.1.2/debian/mans/R_mds.1 1970-01-01 01:00:00.000000000 +0100
+++ seer-1.1.2/debian/mans/R_mds.1 2017-03-23 14:33:36.000000000 +0100
@@ -0,0 +1,32 @@
+.TH R_MDS "1" "March 2017" "R_mds 1.1.2" "User Commands"
+.SH NAME
+R_mds \- project distance matrix into lower number of dimensions
+.SH SYNOPSIS
+.B R_mds
+\fI\,-k <filtered_kmers.txt> -p <pheno_file>\/\fR
+.SH DESCRIPTION
+Projects distance matrix into lower number of dimensions
+Requires R and rhdf5 to be installed, see github wiki for more details
+.SH OPTIONS
+.SS Required
+.TP
+\fB\-d\fR, \fB\-\-dist\fR
+Distance matrix output by kmds
+.TP
+\fB\-p\fR, \fB\-\-pheno\fR
+Phenotype file used by seer
+.SS Optional
+.TP
+\fB\-o\fR, \fB\-\-output\fR
+Output prefix (default 'all_structure')
+.TP
+\fB\-\-pc\fR
+Number of dimensions to project into (default 3)
+.TP
+\fB\-R\fR
+R executable (default 'which R')
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Displays this message
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can
be used for any other usage of the program.
diff -Nru seer-1.1.2/debian/mans/seer.1 seer-1.1.2/debian/mans/seer.1
--- seer-1.1.2/debian/mans/seer.1 2016-12-07 23:05:02.000000000 +0100
+++ seer-1.1.2/debian/mans/seer.1 2017-03-23 14:33:36.000000000 +0100
@@ -1,5 +1,4 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
-.TH SEER "1" "March 2016" "seer 1.1.0" "User Commands"
+.TH SEER "1" "March 2017" "seer 1.1.2" "User Commands"
.SH NAME
seer \- sequence element enrichment analysis
.SH DESCRIPTION
@@ -44,10 +43,6 @@
\fB\-\-min_words\fR arg
minimum kmer occurrences. Overrides \fB\-\-maf\fR
.TP
-\fB\-\-positive_only\fR
-only test words with a predicted positive effect
-direction
-.TP
\fB\-\-chisq\fR arg (=10e\-5)
p\-value threshold for initial chi squared test. Set
to 1 to show all
@@ -61,6 +56,9 @@
print lists of samples significant kmers were found
in
.TP
+\fB\-\-version\fR
+prints version and exits
+.TP
\fB\-h\fR [ \fB\-\-help\fR ]
full help message
.SH EXAMPLES
diff -Nru seer-1.1.2/debian/README.Debian seer-1.1.2/debian/README.Debian
--- seer-1.1.2/debian/README.Debian 2016-12-07 23:05:02.000000000 +0100
+++ seer-1.1.2/debian/README.Debian 2017-03-23 14:33:36.000000000 +0100
@@ -9,4 +9,17 @@
examples/example_wrapper.py
+
+== Renamed Perl scripts ==
+
+In the Debian packaged version the .pl extension was stripped from
+the following scripts:
+
+ blast_top_hits.pl -> blast_top_hits
+ hits_to_fastq.pl -> hits_to_fastq
+ mapping_to_phandango.pl -> mapping_to_phandango
+ mash2matrix.pl -> mash2matrix
+ reformat_output.pl -> reformat_output
+ R_mds.pl -> R_mds
+
-- Andreas Tille <ti...@debian.org> Tue, 29 Mar 2016 19:32:29 +0200
diff -Nru seer-1.1.2/debian/rules seer-1.1.2/debian/rules
--- seer-1.1.2/debian/rules 2016-12-07 23:05:02.000000000 +0100
+++ seer-1.1.2/debian/rules 2017-03-23 14:33:36.000000000 +0100
@@ -13,7 +13,12 @@
override_dh_auto_install:
dh_auto_install -- PREFIX=$(CURDIR)/debian/$(DEBPKGNAME)/usr
- cp -a scripts/blast_top_hits.pl
$(CURDIR)/debian/$(DEBPKGNAME)/usr/bin/blast_top_hits
+ for pl in scripts/*.pl ; do \
+ plbase=`basename $${pl} .pl` ; \
+ sed "s+Usage: ./$${plbase}.pl+Usage: $${plbase}+" $${pl} >
$(CURDIR)/debian/$(DEBPKGNAME)/usr/bin/$${plbase} ; \
+ done
+ # Fix broken usage hint:
+ sed -i "s+Usage: ./hits_to_matrix.pl+Usage: reformat_output+"
$(CURDIR)/debian/$(DEBPKGNAME)/usr/bin/reformat_output
%:
dh $@
