[med-svn] [Git][med-team/trinculo][master] 4 commits: routine-update: Rules-Requires-Root: no
Andreas Tille
gitlab at salsa.debian.org
Fri Apr 10 06:45:09 BST 2020
Andreas Tille pushed to branch master at Debian Med / trinculo
Commits:
7a48b743 by Andreas Tille at 2020-04-10T07:31:20+02:00
routine-update: Rules-Requires-Root: no
- - - - -
2319d83e by Andreas Tille at 2020-04-10T07:39:22+02:00
Add run-unit-test to user documentation
- - - - -
b674547b by Andreas Tille at 2020-04-10T07:42:58+02:00
Fix spelling
- - - - -
c3a0ada2 by Andreas Tille at 2020-04-10T07:43:53+02:00
Upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/docs
- + debian/patches/series
- + debian/patches/spelling.patch
- debian/tests/run-unit-test
- debian/trinculo.1
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+trinculo (0.96+dfsg-2) unstable; urgency=medium
+
+ * Rules-Requires-Root: no (routine-update)
+ * Add run-unit-test to user documentation
+ * Fix spelling
+
+ -- Andreas Tille <tille at debian.org> Fri, 10 Apr 2020 07:43:12 +0200
+
trinculo (0.96+dfsg-1) unstable; urgency=medium
* Initial release (Closes: #955602)
=====================================
debian/control
=====================================
@@ -9,13 +9,14 @@ Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/trinculo
Vcs-Git: https://salsa.debian.org/med-team/trinculo.git
Homepage: https://sourceforge.net/projects/trinculo/
+Rules-Requires-Root: no
Package: trinculo
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
-Description: toolkit to carry out genetic association for multi-catagory phenotypes
- An efficient toolkit for carrying out genetic association for multi-catagory
+Description: toolkit to carry out genetic association for multi-category phenotypes
+ An efficient toolkit for carrying out genetic association for multi-category
phenotypes. Implements multinomial and ordinal association incorporating
covariates, conditional analysis, empirical and non-emperical priors and
fine-mapping.
=====================================
debian/docs
=====================================
@@ -1,2 +1,3 @@
README.txt
debian/README.test
+debian/tests/run-unit-test
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+spelling.patch
=====================================
debian/patches/spelling.patch
=====================================
@@ -0,0 +1,35 @@
+Author: ndreas Tille <tille at debian.org>
+Last-Update: Fri, 10 Apr 2020 07:31:20 +0200
+Description: Fix spelling
+
+--- a/src/inputparser.h
++++ b/src/inputparser.h
+@@ -87,7 +87,7 @@ inputs::inputs(){
+ threads=1;
+
+ usage = "Usage: trinculo MODE [--bfile GENOTYPES_PREFIX | --dosage GENOTYPES.DOSE ] --pheno PHENOTYPES.TXT --phenoname PHENOTYPE [ --basepheno REF --missingpheno MISSING ] [--covar COVARIATES.TXT --normalize] [--priors PRIORS.TXT | --defaultprior --priorsigma PRIORVAR --priorcor PRIORCOR --covarsigma PRIORVAR | --empiricalprior ] [ --select --phenops --errormat --fullmodel --waldstats ] [ --noassoc ] [--threads n] [ --precision DIGITS ] [ --fitIter NITER --fitAbsTol ABSTOL --fitRelTol RELTOL ][--help]";
+- help = "\nUsage:\n trinculo MODE [--bfile GENOTYPES_PREFIX | --dosage GENOTYPES.DOSE ] [--out OUTPUT_PREFIX] --pheno PHENOTYPES.TXT --phenoname PHENOTYPE [--basepheno REF --missingpheno MISSING ] [--covar COVARIATES.TXT --normalize] [--condition SNPS.TXT] [--priors PRIORS.TXT | --defaultprior --priorsigma PRIORVAR --priorcor PRIORCOR --covarsigma PRIORVAR | --empiricalprior ] [ --select --phenops --errormat --fullmodel --waldstats ] [ --noassoc ] [--threads n] [ --precision DIGITS ] [ --fitIter NITER --fitAbsTol ABSTOL --fitRelTol RELTOL ] [--help]\n\nOptions:\n\nMODE\t- Either multinom or ordinal for multinomial or ordinal logistic regression\n\n--bfile FILE_PREFIX\t- Genotype input in binary plink format (FILE_PREFIX.bed, FILE_PREFIX.bim and FILE_PREFIX.fam)\n--dosage FILE\t- Genotype input in dosage format\n--out PREFIX\t- The prefix used for output files [default is \"trinculo\"]\n\n--pheno FILE\t- Phenotype input (same format as plink)--phenoname STRING\t-The phenotype in the phenotype file to analyse\n--basepheno STRING\t- The reference catagory to use for the multinomial analysis [defaults to first catagory encountered]\n--missingpheno STRING\t- The symbol to be use to indicate a missing phenotype in the phenotype file\n\n--condition FILE\t- A file containing a list of SNPs (one per line) to conditon on (i.e. include as covariates)\n\n--covar FILE\t- A file containing covariates to condition on (same format as plink)\n--normalize\t- Normalizes covariates to have a variance of 1 [off by default]\n\n--priors FILE\t- A prior covariance matrix on effect sizes\n--defaultpriors\t- Construct a prior matrix based on default values\n--priorsigma VALUE\t- Set the prior variance on effect sizes within a disease[default is 0.04]\n--priorcor VALUE\t- Set the prior correlation on effect sizes across diseases [default is 0]\n--covarsigma VALUE\t- Prior on the covariate effect size [Default is 1]\n--empiricalprior\t - Calculate an empirical prior directly from the data\n--noassoc\t-do not do any association testing, just infer the prior\n\n--select\t-Do Bayesian model selection (i.e. calculate marginal likelihoods for each sharing model)\n--phenops\t-Do a likelihood ratio test on each phenotype individually\n--waldstats\t-Calculate standard errors, Z scores and Wald p-values\n--errormat\t-Output the variance-covariance matrix for the log odds ratio\n--fullmodel\t-Output all parameter estimates and the full error matrix\n\n--threads n\tUse up to n cores\n\n--precision DIGITS\tPrint output to DIGITS significant figures\n\n--fitIter NITER\tTry up to NITER iterations when fitting models\n--fitAbsTol ABSTOL\tTerminate model fitting if results change by less than ABSTOL\n--fitRelTol RELTOL\tTerminate model fitting if results change by less than (RELTOL x value)\n\n--help\t- Prints this message\n\n";
++ help = "\nUsage:\n trinculo MODE [--bfile GENOTYPES_PREFIX | --dosage GENOTYPES.DOSE ] [--out OUTPUT_PREFIX] --pheno PHENOTYPES.TXT --phenoname PHENOTYPE [--basepheno REF --missingpheno MISSING ] [--covar COVARIATES.TXT --normalize] [--condition SNPS.TXT] [--priors PRIORS.TXT | --defaultprior --priorsigma PRIORVAR --priorcor PRIORCOR --covarsigma PRIORVAR | --empiricalprior ] [ --select --phenops --errormat --fullmodel --waldstats ] [ --noassoc ] [--threads n] [ --precision DIGITS ] [ --fitIter NITER --fitAbsTol ABSTOL --fitRelTol RELTOL ] [--help]\n\nOptions:\n\nMODE\t- Either multinom or ordinal for multinomial or ordinal logistic regression\n\n--bfile FILE_PREFIX\t- Genotype input in binary plink format (FILE_PREFIX.bed, FILE_PREFIX.bim and FILE_PREFIX.fam)\n--dosage FILE\t- Genotype input in dosage format\n--out PREFIX\t- The prefix used for output files [default is \"trinculo\"]\n\n--pheno FILE\t- Phenotype input (same format as plink)--phenoname STRING\t-The phenotype in the phenotype file to analyse\n--basepheno STRING\t- The reference category to use for the multinomial analysis [defaults to first category encountered]\n--missingpheno STRING\t- The symbol to be use to indicate a missing phenotype in the phenotype file\n\n--condition FILE\t- A file containing a list of SNPs (one per line) to conditon on (i.e. include as covariates)\n\n--covar FILE\t- A file containing covariates to condition on (same format as plink)\n--normalize\t- Normalizes covariates to have a variance of 1 [off by default]\n\n--priors FILE\t- A prior covariance matrix on effect sizes\n--defaultpriors\t- Construct a prior matrix based on default values\n--priorsigma VALUE\t- Set the prior variance on effect sizes within a disease[default is 0.04]\n--priorcor VALUE\t- Set the prior correlation on effect sizes across diseases [default is 0]\n--covarsigma VALUE\t- Prior on the covariate effect size [Default is 1]\n--empiricalprior\t - Calculate an empirical prior directly from the data\n--noassoc\t-do not do any association testing, just infer the prior\n\n--select\t-Do Bayesian model selection (i.e. calculate marginal likelihoods for each sharing model)\n--phenops\t-Do a likelihood ratio test on each phenotype individually\n--waldstats\t-Calculate standard errors, Z scores and Wald p-values\n--errormat\t-Output the variance-covariance matrix for the log odds ratio\n--fullmodel\t-Output all parameter estimates and the full error matrix\n\n--threads n\tUse up to n cores\n\n--precision DIGITS\tPrint output to DIGITS significant figures\n\n--fitIter NITER\tTry up to NITER iterations when fitting models\n--fitAbsTol ABSTOL\tTerminate model fitting if results change by less than ABSTOL\n--fitRelTol RELTOL\tTerminate model fitting if results change by less than (RELTOL x value)\n\n--help\t- Prints this message\n\n";
+ normalizecovar = 0;
+ modelSelect = 0;
+ dosagefile = "";
+--- a/README.txt
++++ b/README.txt
+@@ -2,7 +2,7 @@
+ ##### trinculo v0.96, January 2016 ######
+ ###############################
+
+-Welcome to trinculo v0.96. This program contains tools to carry out multicatagory regression analyses, including multinomial and proportional odds ordinal logistic scans, conditional multinomial analysis, Bayesian multinomial logistic regression and multinomial fine-mapping.
++Welcome to trinculo v0.96. This program contains tools to carry out multicategory regression analyses, including multinomial and proportional odds ordinal logistic scans, conditional multinomial analysis, Bayesian multinomial logistic regression and multinomial fine-mapping.
+
+ Table of contents of this README.txt:
+
+@@ -59,7 +59,7 @@ MODE - Either multinom or ordinal for mu
+ --out PREFIX - The prefix used for output files [default is "trinculo"]
+
+ --pheno FILE - Phenotype input (same format as plink)--phenoname STRING -The phenotype in the phenotype file to analyse
+---basepheno STRING - The reference catagory to use for the multinomial analysis [defaults to first catagory encountered]
++--basepheno STRING - The reference category to use for the multinomial analysis [defaults to first category encountered]
+ --missingpheno STRING - The symbol to be use to indicate a missing phenotype in the phenotype file
+
+ --condition FILE - A file containing a list of SNPs (one per line) to conditon on (i.e. include as covariates)
=====================================
debian/tests/run-unit-test
=====================================
@@ -6,9 +6,6 @@ pkg=trinculo
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
- # Double quote below to expand the temporary directory variable now versus
- # later is on purpose.
- # shellcheck disable=SC2064
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
@@ -16,7 +13,6 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
-#do_stuff_to_test_package#
echo "1. Testing frequentist association (plink)..."
trinculo multinom --bfile genotypes --pheno phenos.txt --phenoname Pheno --basepheno Control
echo "PASSED"
=====================================
debian/trinculo.1
=====================================
@@ -1,7 +1,7 @@
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
.TH TRINCULO "1" "April 2020" "trinculo 0.96" "User Commands"
.SH NAME
-trinculo \- toolkit to carry out genetic association for multi-catagory phenotypes
+trinculo \- toolkit to carry out genetic association for multi-category phenotypes
.SH DESCRIPTION
Running a multinomial logistic analysis
.SS "Usage:"
@@ -16,7 +16,7 @@ MODE \- Either multinom or ordinal for multinomial or ordinal logistic regres
\fB\-\-out\fR PREFIX \- The prefix used for output files [default is "trinculo"]
.PP
\fB\-\-pheno\fR FILE \- Phenotype input (same format as plink)\-\-phenoname STRING \fB\-The\fR phenotype in the phenotype file to analyse
-\fB\-\-basepheno\fR STRING \- The reference catagory to use for the multinomial analysis [defaults to first catagory encountered]
+\fB\-\-basepheno\fR STRING \- The reference category to use for the multinomial analysis [defaults to first category encountered]
\fB\-\-missingpheno\fR STRING \- The symbol to be use to indicate a missing phenotype in the phenotype file
.PP
\fB\-\-condition\fR FILE \- A file containing a list of SNPs (one per line) to conditon on (i.e. include as covariates)
View it on GitLab: https://salsa.debian.org/med-team/trinculo/-/compare/2a6cff05aa20d910c078dab9b8a2aa93c1f1dbd4...c3a0ada2931a3eddb23ba1dd1dad245bd4f4b464
--
View it on GitLab: https://salsa.debian.org/med-team/trinculo/-/compare/2a6cff05aa20d910c078dab9b8a2aa93c1f1dbd4...c3a0ada2931a3eddb23ba1dd1dad245bd4f4b464
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