[med-svn] [Git][med-team/qtltools][master] 2 commits: Install the new files in appropriate locations.

Tue Oct 13 16:57:09 BST 2020


Michael R. Crusoe pushed to branch master at Debian Med / qtltools


Commits:
1bab2a47 by Michael R. Crusoe at 2020-10-13T15:40:32+02:00
Install the new files in appropriate locations.

- - - - -
574bb232 by Michael R. Crusoe at 2020-10-13T17:56:42+02:00
release 1.3.1+dfsg-2

- - - - -


4 changed files:

- − debian/QTLtools.1
- debian/changelog
- debian/qtltools.install
- debian/qtltools.manpages


Changes:

=====================================
debian/QTLtools.1 deleted
=====================================
@@ -1,100 +0,0 @@
-.\"
-.TH QTLtools "1" "November 2016" "1.0"
-.SH NAME
-QTLtools \- Tool set for molecular QTL discovery and analysis
-.SH SYNOPSIS
-.B QTLtools [\fImode\fR] [\fIoptions\fR]
-.SH DESCRIPTION
-QTLtools is a tool set for molecular QTL discovery and analysis.
-It allows user to go from the raw sequence data to collection of molecular
-Quantitative Trait Loci (QTLs) in few easy-to-perform steps.
-.SH MODE
-.TP
-\fBbamstat\fR
-Calculate basic QC metrics for BAM/SAM.
-.br
-To check the quality of some sequence data by counting the number of reads mapped to the reference genome and falling within a reference annotation.
-.TP
-\fBmatch\fR
-Match VCF genotypes to BAM/SAM file.
-.br
-To ensure good match between the sequence and genotype data.
-This is useful to detect sample mislabeling, contamination or PCR amplification biases.
-.TP
-\fBquan\fR
-Quantification mode.
-.br
-To quantify exon and gene expression levels given a reference annotation such as GENCODE.
-.TP
-\fBpca\fR
-Calculate principal components for a BED/VCF/BCF file.
-.br
-To perform Principal Component Analysis (PCA) on genotype or molecular phenotype data.
-.TP
-\fBcis\fR
-cis QTL analysis.
-.br
-To map molecular Quantitative Trait Loci (mQTLs) in cis (i.e. proximal to the phenotype).
-This mode extends FastQTL by including two additional options: (i) to study groups of phenotypes such as genes containing multiple exons or (ii) to perform conditional analysis in order to discover multiple mQTLs per phenotype.
-.TP
-\fBtrans\fR
-trans QTL analysis.
-.br
-To map QTLs in trans.
-This can be done either using a full permutation scheme or with a much quicker approximation.
-.TP
-\fBfdensity\fR
-Functional density around QTLs.
-.br
-To measure the density of functional annotations around the QTL locations.
-Useful to look at the degree of overlap between QTLs and functional annotations.
-.TP
-\fBfenrich\fR
-Functional enrichment for QTLs.
-.br
-To measure how QTLs are enriched in any given functional annotations.
-.TP
-\fBrtc\fR
-Regulatory Trait Concordance analysis.
-.br
-To co-localize collections of QTLs with collection of GWAS hits.
-
-.SH OPTIONS
-.TP
-\fB\-\-help\fR
-.br
-Print help about options for the selected mode.
-
-.SH EXAMPLE
-
-\fBQTLtools\fR \fBbamstat\fR --help
-
-\fBQTLtools\fR \fBbamstat\fR --bam HG00381.chr22.bam --bed gencode.v19.exon.chr22.bed.gz --filter-mapping-quality 150 --out HG00381.chr22.bamstat.txt
-.br
-\fBQTLtools\fR \fBmatch\fR --bam HG00381.chr22.bam --vcf genotypes.chr22.vcf.gz --filter-mapping-quality 150 --out HG00381.chr22.bamstat.txt
-.br
-\fBQTLtools\fR \fBquan\fR --bam HG00381.chr22.bam --gtf gencode.v19.annotation.chr22.gtf.gz --samples HG00381 --out-prefix HG00381 --filter-mapping-quality 150 --filter-mismatch 5 --filter-mismatch-total 5 --rpkm --no-merge
-.br
-\fBQTLtools\fR \fBpca\fR --bed genes.50percent.chr22.bed.gz --scale --center --out genes.50percent.chr22
-.br
-\fBQTLtools\fR \fBcis\fR --vcf genotypes.chr22.vcf.gz --bed genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --nominal 0.01 --region chr22:17000000-18000000 --out nominals.txt
-.br
-\fBQTLtools\fR \fBcis\fR --vcf genotypes.chr22.vcf.gz --bed genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --permute 1000 --region chr22:17000000-18000000 --out permutations.txt
-.br
-\fBQTLtools\fR \fBcis\fR --vcf genotypes.chr22.vcf.gz --bed genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --mapping permutations_all.thresholds.txt --chunk 12 16 --out conditional_12_16.txt
-.br
-\fBQTLtools\fR \fBtrans\fR --vcf genotypes.chr22.vcf.gz --bed genes.simulated.chr22.bed.gz --nominal --threshold 1e-5 --out trans.nominal 
-.br
-\fBQTLtools\fR \fBtrans\fR --vcf genotypes.chr22.vcf.gz --bed genes.simulated.chr22.bed.gz --sample 1000 --normal --out trans.sample 
-.br
-\fBQTLtools\fR \fBfdensity\fR --qtl results.genes.significant.bed --bed TFs.encode.bed.gz --out density.TF.around.QTL.txt 
-.br
-\fBQTLtools\fR \fBfenrich\fR --qtl results.genes.significant.bed --tss results.genes.quantified.bed --bed TFs.encode.bed.gz --out enrichement.QTL.in.TF.txt 
-.br
-\fBQTLtools\fR \fBrtc\fR --vcf genotypes.chr22.vcf.gz --bed genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --hotspot hotspots_b37_hg19.bed --gwas-cis GWAS.b37.txt permutations_all.significant.txt --normal --out rtc_results.txt 
-.br
-
-.SH SEE ALSO
-.BR https://qtltools.github.io/qtltools/
-.SH AUTHOR
-QTLtools was written by Olivier Delaneau, Halit Ongen and Manolis Dermitzakis.


=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+qtltools (1.3.1+dfsg-2) unstable; urgency=medium
+
+  * Team upload.
+  * Install the new files in appropriate locations.
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Tue, 13 Oct 2020 17:56:30 +0200
+
 qtltools (1.3.1+dfsg-1) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/qtltools.install
=====================================
@@ -1 +1,3 @@
 bin/QTLtools	usr/bin/
+etc/bash_completion.d/QTLtools_bash_autocomplete.bash
+usr/local/bin/* usr/bin/


=====================================
debian/qtltools.manpages
=====================================
@@ -1 +1 @@
-debian/QTLtools.1
+usr/local/share/man/man1/*.1



View it on GitLab: https://salsa.debian.org/med-team/qtltools/-/compare/b25e46a3d429aaa46f3e55ed1807c159e09fbe0d...574bb2324b154ad20a47becf2a6c25087d3a8894

-- 
View it on GitLab: https://salsa.debian.org/med-team/qtltools/-/compare/b25e46a3d429aaa46f3e55ed1807c159e09fbe0d...574bb2324b154ad20a47becf2a6c25087d3a8894
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20201013/d3e16051/attachment-0001.html>
