Added canu 1.5

.github/workflows/main.yml

@@ -0,0 +1,44 @@
+name: Singularity build
+on: [push, pull_request]
+jobs:
+
+  build:
+    name: Build
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        singularity_version:
+          - '3.7.3'
+    container:
+      image: quay.io/singularity/singularity:v${{ matrix.singularity_version }}
+      options: --privileged
+    steps:
+    - name: Check out code for the container build
+      uses: actions/checkout@v1
+
+    - name: Install useful utilities
+      run: apk update && apk add --no-cache tree figlet wget
+
+    - name: Build and test container
+      run: |
+       for DIRECTORY in *
+       do
+         if [ -d $DIRECTORY ]; then
+            if [[ $DIRECTORY != 'images' ]]; then
+                cd $DIRECTORY
+
+                if [ ! -f .ignore ]; then
+                    echo "Building container"
+                    bash ./build.sh
+
+                    if [ -f ./test.sh ]; then
+                        echo "Running tests"
+                        bash ./test.sh
+                    else
+                        echo "Test file not found. Skipping tests."
+                    fi
+                fi
+            cd ..
+           fi
+         fi
+        done

.github/workflows/pretty.yml

@@ -0,0 +1,109 @@
+name: Publishing ready
+on: [push, pull_request]
+jobs:
+  build:
+    name: Build
+    runs-on: ubuntu-18.04
+    steps:
+    - name: Check out code
+      uses: actions/checkout@v2
+
+    - name: Install useful utilities
+      run: sudo apt-get install -y tree
+
+    - name: Checking if LICENSE exists
+      run: |
+        FILE=LICENSE
+        if [ -f "$FILE" ]; then
+            echo "File "$FILE" exists."
+            exit 0
+        else 
+            echo "File $FILE does not exist."
+            exit 1
+        fi
+
+    - name: Checking if Apache License Version 2.0, January 2004 is being used
+      run: |
+        if grep --quiet "Apache License" LICENSE && grep --quiet "Version 2.0, January 2004" LICENSE; then
+            echo "Using Apache License Version 2.0, January 2004"
+            exit 0
+        else
+            echo "Not using Apache License Version 2.0, January 2004"
+            exit 1
+        fi
+    
+    - name: Checking if CONTRIBUTING guide exists
+      run: |
+        FILE=CONTRIBUTING.md
+        if [ -f "$FILE" ]; then
+            echo "File "$FILE" exists."
+            exit 0
+        else 
+            echo "File $FILE does not exist."
+            exit 1
+        fi
+
+    - name: Checking if README file exists
+      run: |
+        FILE=README.md
+        if [ -f "$FILE" ]; then
+            echo "File "$FILE" exists."
+            exit 0
+        else 
+            echo "File $FILE does not exist."
+            exit 1
+        fi
+    
+    - name: Checking if copyrighted to Pittsburgh Supercomputing Center
+      run: |
+        if grep --quiet "Pittsburgh Supercomputing Center. All Rights Reserved." README.md; then
+            echo "Copyright (c) Pittsburgh Supercomputing Center"
+            exit 0
+        else
+            echo "No reference to Pittsburgh Supercomputing Center"
+            exit 1
+        fi
+
+    - name: Checking if there exists at least one Singularity definition file
+      run: |
+        FILE=Singularity
+        if [ $(find . -name "$FILE" -mmin -5 | wc -l) -gt 0 ]; then 
+            echo "File "$FILE" was found.";
+            exit 0 
+        else 
+            echo "File "$FILE" was not found.";
+            exit 1
+        fi
+
+    - name: Checking if there exists at least one build script
+      run: |
+        FILE=build.sh
+        if [ $(find . -name "$FILE" -mmin -5 | wc -l) -gt 0 ]; then 
+            echo "File "$FILE" was found.";
+            exit 0 
+        else 
+            echo "File "$FILE" was not found.";
+            exit 1
+        fi
+
+    - name: Checking if there exists at least one remote build script
+      run: |
+        FILE=rbuild.sh
+        if [ $(find . -name "$FILE" -mmin -5 | wc -l) -gt 0 ]; then 
+            echo "File "$FILE" was found.";
+            exit 0 
+        else 
+            echo "File "$FILE" was not found.";
+            exit 1
+        fi
+
+    - name: Checking if there exists at least one test script
+      run: |
+        FILE=test.sh
+        if [ $(find . -name "$FILE" -mmin -5 | wc -l) -gt 0 ]; then 
+            echo "File "$FILE" was found.";
+            exit 0 
+        else 
+            echo "File "$FILE" was not found.";
+            exit 1
+        fi

1.5/Singularity

@@ -0,0 +1,17 @@
+Bootstrap: docker
+From: continuumio/anaconda3
+
+%labels
+    AUTHOR icaoberg
+    EMAIL [email protected]
+    SUPPORT [email protected]
+    REPOSITORY http://gitub.com/pscedu/singularity-canu
+    COPYRIGHT Copyright © 2024 Pittsburgh Supercomputing Center. All Rights Reserved.
+    VERSION 1.5
+
+%post
+    apt update
+    conda install -c conda-forge -c bioconda -c defaults canu
+
+%runscript
+    canu "$@"

1.5/build.sh

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+#!/bin/bash
+
+IMAGE=singularity-canu-1.5.sif
+DEFINITION=Singularity
+
+if [ -f $IMAGE ]; then
+	rm -fv $IMAGE
+fi
+
+singularity build $IMAGE $DEFINITION
+
+if [ -f $IMAGE ]; then
+	exit 0
+else
+	exit 1
+fi

1.5/canu

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+VERSION=1.5
+PACKAGE=canu
+TOOL=canu
+DIRECTORY=$(dirname $0)
+
+STORAGES=(/ocean /bil /hive /local)
+
+OPTIONS=""
+for STORAGE in "${STORAGES[@]}"
+do
+	if [ -d "$STORAGE" ]; then
+		OPTIONS=$OPTIONS" -B $STORAGE"
+	fi
+done
+
+singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@"

1.5/modulefile.lua

@@ -0,0 +1,39 @@
+--
+-- canu 1.5 modulefile
+--
+-- "URL: https://www.psc.edu/resources/software"
+-- "Category: Utilities"
+-- "Description: ."
+-- "Keywords: singularity bioinformatics"
+
+whatis("Name: canu")
+whatis("Version: 1.5")
+whatis("Category: Utilities")
+whatis("URL: https://www.psc.edu/resources/software")
+whatis("Description: A single molecule sequence assembler for genomes large and small.")
+whatis("Keywords: singularity bioinformatics")
+
+help([[
+A single molecule sequence assembler for genomes large and small.
+
+To load the module, type
+
+> module load canu/1.5
+
+To unload the module, type
+
+> module unload canu/1.5
+
+For help, type
+
+> canu -h
+
+Tools included in this module are
+
+* canu
+]])
+
+local package = "canu"
+local version = "1.5"
+local base    = pathJoin("/opt/packages",package,version)
+prepend_path("PATH", base)

1.5/rbuild.sh

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+#!/bin/bash
+
+IMAGE=singularity-canu-1.5.sif
+DEFINITION=Singularity
+
+if [ -f $IMAGE ]; then
+	rm -fv $IMAGE
+fi
+
+singularity build --remote $IMAGE $DEFINITION
+
+if [ -f $IMAGE ]; then
+	exit 0
+else
+	exit 1
+fi

1.5/test.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+set -x
+
+tree .