[med-svn] [Git][med-team/pftools][upstream] New upstream version 3.2.11

Andreas Tille (@tille) gitlab at salsa.debian.org
Tue Jan 25 09:17:03 GMT 2022 


Andreas Tille pushed to branch upstream at Debian Med / pftools


Commits:
3ea320c1 by Andreas Tille at 2022-01-25T09:58:30+01:00
New upstream version 3.2.11
- - - - -


6 changed files:

- .gitignore
- CMakeLists.txt
- Docker/README.docker
- README.md
- src/C/config.h.cmake
- tests/examples/test_V3.sh.cmake


Changes:

=====================================
.gitignore
=====================================
@@ -1,4 +1,5 @@
 build/
+testing/
 
 \.kdev4/
 


=====================================
CMakeLists.txt
=====================================
@@ -1,10 +1,10 @@
 #########################################################################################
 # PfTools versioning
 #
-SET(VERSION "3.2.8")
+SET(VERSION "3.2.11")
 SET(MAJOR_VERSION "3")
 SET(MINOR_VERSION "2")
-SET(PATCH_VERSION "8")
+SET(PATCH_VERSION "11")
 SET(DATA_PATH "share/data"     CACHE STRING "Installation data folder" )
 SET(DOC_PATH  "share/doc"      CACHE STRING "Installation doc folder" )
 SET(MAN1_PATH "share/man/man1" CACHE STRING "Installation man1 folder" )
@@ -396,7 +396,7 @@ ADD_SUBDIRECTORY(data)
 #########################################################################################
 # Enabling TESTING
 include(CTest)
-SET(TESTS_DIRECTORY "${PROJECT_SOURCE_DIR}/Tests" CACHE PATH "Directory for tests")
+SET(TESTS_DIRECTORY "${PROJECT_SOURCE_DIR}/testing" CACHE PATH "Directory for tests")
 SET(TESTS_DATA_DIR "${PROJECT_SOURCE_DIR}/tests")
 IF (NOT EXISTS "${TESTS_DIRECTORY}" )
 	FILE(MAKE_DIRECTORY "${TESTS_DIRECTORY}" )


=====================================
Docker/README.docker
=====================================
@@ -1,5 +1,5 @@
 # Build Docker image
-export PFTOOLS_VERSION=3.2.6
+export PFTOOLS_VERSION=3.2.11
 docker build -t pftools:$PFTOOLS_VERSION --no-cache=true --build-arg BUILD_DATE=$(date -u +'%Y-%m-%dT%H:%M:%SZ') --build-arg PFTOOLS_VERSION=$PFTOOLS_VERSION -f Dockerfile .  2>&1 >pftools.Dockerfile.log
 
 


=====================================
README.md
=====================================
@@ -1,4 +1,24 @@
-# PfTools   v3.2
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pftools/README.html)
+[![Anaconda-Server Badge](https://anaconda.org/bioconda/pftools/badges/license.svg)](https://anaconda.org/bioconda/pftools)
+[![Anaconda-Server Badge](https://img.shields.io/conda/dn/bioconda/pftools.svg?style=flat)](https://anaconda.org/bioconda/pftools)
+
+PfTools
+=========================================
+
+## Table of Contents
+
+   * [Foreword](#foreword)
+   * [Installation](#installation)
+     * [Using Docker](#using-docker)
+     * [Using Singularity](#using-singularity)
+     * [Bioconda](#bioconda)
+     * [Manually](#manually) 
+   * [Generalized profile syntax](#generalized-profile-syntax)
+   * [Algorithms description](#algorithms-description)
+   * [Applications of the Pftools](#applications-of-the-pftools)
+   * [Authors](#authors)
+
+# Foreword
 
 (C) Copyright SIB Swiss Institute of Bioinformatics
 available from  https://github.com/sib-swiss/pftools3 under GPL v2. See LICENSE.
@@ -7,9 +27,86 @@ available from  https://github.com/sib-swiss/pftools3 under GPL v2. See LICENSE.
 Version 3 contains the original FORTRAN 77 pftools (release 2.3)
 and the new pftoolsV3 programs.
 
-The 'pftools' package documententation is unfortunately scattered over many
-different places. Here is an annotated list of the relevant documents we are
-aware of:
+# Installation
+
+### Using Docker
+
+First you must have [Docker](https://docs.docker.com/get-docker/) installed and running.  
+Secondly have a look at the availabe pftools biocontainers at [quay.io](https://quay.io/repository/biocontainers/pftools?tab=tags) or at [Docker Hub](https://hub.docker.com/r/sibswiss/pftools).  
+Then:
+  ```
+# get the chosen pftools container version
+docker pull quay.io/biocontainers/pftools:2.3.5--h4333106_0
+   or
+docker pull sibswiss/pftools:3.2.8
+# use an pftools's tool e.g. pfscan 
+docker run quay.io/biocontainers/pftools:2.3.5--h4333106_0 pfscan -h
+   or
+docker run sibswiss/pftools:3.2.8 pfscan -h
+  ```
+
+### Using Singularity
+
+First you must have [Singularity](https://sylabs.io/guides/master/user-guide/quick_start.html) installed and running.
+Secondly have a look at the availabe pftools biocontainers at [quay.io](https://quay.io/repository/biocontainers/pftools?tab=tags) or at [Docker Hub](https://hub.docker.com/r/sibswiss/pftools).  
+Then:
+```
+# get the chosen pftools container version
+singularity pull docker://quay.io/biocontainers/quay.io/biocontainers/pftools:2.3.5--h4333106_0
+   or
+singularity pull docker://sibswiss/pftools:3.2.8
+# run the container
+singularity run pftools_2.3.5--h4333106_0.sif
+```
+
+You are now in the container. You can use an pftools's tool e.g. pfscan doing 
+```
+pfscan -h
+```
+
+## Bioconda
+
+```
+conda install -c bioconda pftools
+```
+
+## Manually
+
+See [here](./INSTALL) for more information
+
+**Prerequisite**  
+
+  * cmake >= 3.7
+  * gcc   >= 4.6
+  * gfortran (or g77 or f77)  for release 2.3 source code
+  * perl  >= 5.5.3   
+    * File::Slurp
+
+**BUILD**  
+```
+git clone https://github.com/sib-swiss/pftools3.git
+cd pftools3
+mkdir build
+cd build/
+cmake ..
+```
+
+**COMPILE**  
+```
+make
+```
+
+**INSTALL**  
+```
+make install
+```
+
+**CHECK/TEST**  
+```
+make test
+```
+
+After installation, in the share/examples/ subdirectory, the *test_V3.sh* shell script is a good starting point for using pfsearchV3/pfscanV3.
 
 # Generalized profile syntax
 
@@ -27,10 +124,6 @@ it was originally published in
   PubMed PMID: [7584418](https://www.ncbi.nlm.nih.gov/pubmed/7584418).
 
 
-# Command-line tutorial
-
-After installation, in the share/examples/ subdirectory, the *test_V3.sh* shell script is a good starting point for using pfsearchV3/pfscanV3.
-
 # Algorithms description
 
 Technical details about how profiles can be constructed and parametrized


=====================================
src/C/config.h.cmake
=====================================
@@ -10,11 +10,9 @@
 #define __USE_WINAPI__
 #endif
 
-#cmakedefine USE_AFFINITY
-#if defined(USE_AFFINITY)
-# if defined(__GNUC__) && !defined(USE_WINAPI)
-#  define _GNU_SOURCE
-# endif
+/* NOTE Compilation fails if _GNU_SOURCE is not defined with affinity off */
+#if defined(__GNUC__) && !defined(USE_WINAPI)
+# define _GNU_SOURCE
 #endif
 
 /*


=====================================
tests/examples/test_V3.sh.cmake
=====================================
@@ -127,11 +127,11 @@ $PFSCANV3   -n -t 1 -q ./hiv.prf ./hiv.fastq     # FASTQ
 #
 # Default output mode:
 #----------------------------------------------------------------------#
-$PFSEARCH      -f ./sh3.prf ./VAV_HUMAN.seq | sort -nr > $TMPDIR/sh3.VAV_HUMAN.2.hit
+$PFSEARCH                    -f ./sh3.prf ./VAV_HUMAN.seq | sort -nr > $TMPDIR/sh3.VAV_HUMAN.2.hit
 $PFSEARCHV3 -n -f ./sh3.prf ./VAV_HUMAN.seq | sort -nr > $TMPDIR/sh3.VAV_HUMAN.3.hit
 diff -b $TMPDIR/sh3.VAV_HUMAN.2.hit $TMPDIR/sh3.VAV_HUMAN.3.hit # expecting no difference
 
-$PFSEARCH      -fb ./ecp.prf $TMPDIR/CVPBR322.fa | sort -nr > $TMPDIR/ecp.CVPBR322.2.hit
+$PFSEARCH                    -fb ./ecp.prf $TMPDIR/CVPBR322.fa | sort -nr > $TMPDIR/ecp.CVPBR322.2.hit
 $PFSEARCHV3 -n -fb ./ecp.prf $TMPDIR/CVPBR322.fa | sort -nr > $TMPDIR/ecp.CVPBR322.3.hit
 diff -b $TMPDIR/ecp.CVPBR322.2.hit $TMPDIR/ecp.CVPBR322.3.hit  # expecting no difference
 



View it on GitLab: https://salsa.debian.org/med-team/pftools/-/commit/3ea320c1dac134178ce64762c5e234db51c0ee15

-- 
View it on GitLab: https://salsa.debian.org/med-team/pftools/-/commit/3ea320c1dac134178ce64762c5e234db51c0ee15
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