[med-svn] [Git][med-team/pscan-tfbs][master] General review and upload.
Steffen Möller
gitlab at salsa.debian.org
Thu May 3 11:26:03 BST 2018
Steffen Möller pushed to branch master at Debian Med / pscan-tfbs
Commits:
3808e787 by Steffen Moeller at 2018-05-03T12:20:04+02:00
General review and upload.
- - - - -
6 changed files:
- debian/changelog
- + debian/manpages
- + debian/pscan-tfbs.install
- debian/pscan.1
- − debian/pscan.substvars
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,19 +1,16 @@
-pscan-tfbs (1.4-1) UNRELEASED; urgency=low
+pscan-tfbs (1.2.2-1) unstable; urgency=low
[ Steffen Moeller ]
* Initial release (Closes: #673182)
* Added man page
* Homepage claims that version 1.4 exists but I can not find it
- (Andreas Tille Mon, 18 Dec 2017 21:19:24 +0100)
+ (Andreas Tille, Mon, 18 Dec 2017 21:19:24 +0100)
+ Presumably this refers to the web site more than to the
+ C code that seems untouched since ever.
+ (Steffen Moeller, Thu, 03 May 2018 12:05:41 +0200)
+ * Applying link-time optimisation
[ Andreas Tille ]
* Moved packaging from SVN to Git
- -- Steffen Moeller <moeller at debian.org> Wed, 16 May 2012 18:59:59 +0200
-
-pscan-tfbs (1.2.2-1) UNRELEASED; urgency=low
-
- * Download archive contains cpp file with version string 1.2.2
-
- -- Steffen Moeller <moeller at debian.org> Wed, 16 May 2012 18:59:59 +0200
-
+ -- Steffen Moeller <moeller at debian.org> Thu, 03 May 2018 12:06:24 +0200
=====================================
debian/manpages
=====================================
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/pscan.1
=====================================
debian/pscan-tfbs.install
=====================================
--- /dev/null
+++ b/debian/pscan-tfbs.install
@@ -0,0 +1 @@
+pscan usr/bin
=====================================
debian/pscan.1
=====================================
--- a/debian/pscan.1
+++ b/debian/pscan.1
@@ -34,21 +34,21 @@ that are characteristic for the binding of proteins, i.e. transcription factors,
that control the tissue- and situation-dependent expression of a gene.
The tool is supported by the JASPAR database and other data that is downloadable
from the tool's home page.
-.no
+.nh
.PP
.hy
The command line tool
.B pscan
is meant for bulk submission. The tool is also offered with a web
interface that has all auxillary data updated.
-.no
+.nh
.SH OPTIONS
.hy
.B pscan
options only have single dashes (`-') and (with notable
exceptions) followed by a single letter. Options are case-sensitive.
A summary of options is included below.
-.no
+.nh
.TP
.B \-h
Show summary of options similar to this man page.
@@ -115,7 +115,7 @@ This is useful when you have duplicated sequences in your background that may in
The sequences to be used with Pscan have to be promoter sequences.
To obtain meaningful results it's critical that the background and the foreground sequences are consistent between them either in size
and in position (with respect to the transcription start site). For optimal results the foreground set should be a subset of the background set.
-.no
+.nh
.PP
If the "-l" option is not used Pscan will try to find Jaspar/Transfac matrix files in the current folder.
Jaspar files have ".pfm" extension while Transfac ones have ".pro" extension.
@@ -133,7 +133,7 @@ It is handy to use that command the first time one uses a set of matrices with a
A file called human_450_50.short_matrix will be written and it can be used from now on every time you want to use
the same background sequences with the same set of matrices. A file called human_450_50.index will be written too
and it will be useful every time you will use the same background file.
-.no
+.nh
.PP
.B 2)
pscan \-q human_nfy_targets.fasta \-m human_450_50.short_matrix \-ui human_450_50.index
@@ -149,7 +149,7 @@ The output will be a file called "human_nfy_targets.fasta.res" where you will fi
The lower the P-value obtained by a matrix, the higher are the chances that the transcription factor associated to that matrix
is a regulator of the input promoter sequences.
The fields of the output are the following: "Transcription Factor Name", "Matrix ID", "Z Score", "Pvalue", "Foreground Average", "Background Average".
-.no
+.nh
.PP
.B 3)
pscan -q human_nfy_targets.fasta -M MA0108.pfm
@@ -160,7 +160,7 @@ The result will be written in a file called "human_nfy_targets.fasta.ris" where
sorted by a descending score (between 1 and 0). The higher the score, the better is the oligo found with respect to the used matrix.
The fields of the output are the following: "Sequence Header", "Score", "Position from the end of sequence", "Oligo that obtained the score",
"Strand where the oligo was found".
-.no
+.nh
.PP
.B 4)
pscan -p human_450_50.fasta -bi -l matrixfile.wil
@@ -168,7 +168,7 @@ pscan -p human_450_50.fasta -bi -l matrixfile.wil
.hy
This command is like Example #1 with the difference that the matrices set to be used is the one contained in the "matrixfile.wil" file.
Please look at the "example_matrix_file.wil" file included in this Pscan distribution to see the correct format for matrices file.
-.no
+.nh
.PP
.B 5)
pscan -q human_nfy_targets.fasta -l matrixfile.wil -N MATRIX1
=====================================
debian/pscan.substvars deleted
=====================================
--- a/debian/pscan.substvars
+++ /dev/null
@@ -1,2 +0,0 @@
-shlibs:Depends=libc6 (>= 2.2.5), libgcc1 (>= 1:4.1.1), libgsl0ldbl (>= 1.9), libstdc++6 (>= 4.2.1)
-misc:Depends=
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -1,9 +1,16 @@
#!/usr/bin/make -f
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
+
+export DH_VERBOSE=1
+
+CXXFLAGS += -flto
+LDFLAGS += -Wl,-flto
%:
dh $@
override_dh_auto_build:
- g++ -g pscan.cpp -o pscan -O3 -lgsl -lgslcblas
+ $(CXX) $(CXXFLAGS) pscan.cpp -o pscan $(LDFLAGS) -lgslcblas -lgsl
+
+override_dh_auto_clean:
+ dh_clean
+ rm -f pscan
View it on GitLab: https://salsa.debian.org/med-team/pscan-tfbs/commit/3808e787e900ac648b7bb371218408f7a79052a4
---
View it on GitLab: https://salsa.debian.org/med-team/pscan-tfbs/commit/3808e787e900ac648b7bb371218408f7a79052a4
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