Merge pull request #5 from ncbi/dev

Update README and tests for binary distribution

.github/workflows/binary.yml

@@ -0,0 +1,29 @@
+name: binary tarball
+
+on: 
+    workflow_dispatch:
+    release:
+        branches: [ master ]
+    repository_dispatch:
+        types: [linux-binary-test, install-test]
+    schedule: 
+        - cron: '15  15  *   *   *' # 3:15pm every day
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+        - uses: actions/checkout@v4
+        - name: prerequisites
+          run: |
+              sudo apt-get update
+              sudo apt-get install -y ncbi-blast+ 
+              echo "TERM=-$TERM-"
+        - name: download
+          run: bash -x .github/workflows/get_binary_release.sh | tee | tail -1 > dirname
+        - name: 
+          run: stxtyper_v*/stxtyper -v
+        - name: run tests included with distribution
+          run: |
+              directory=$(cat dirname)
+              cd $directory
+              ./test_stxtyper.sh

.github/workflows/get_binary_release.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+# found and lightly modified these functions
+get_latest_release() {
+    curl --silent "https://api.github.com/repos/$1/releases/latest" |
+    grep '"tag_name":' |
+    cut -d '"' -f 4
+}
+
+get_tarball_url() {
+    curl --silent "https://api.github.com/repos/$1/releases/latest" |
+        fgrep '"browser_download_url":' |
+        cut -d '"' -f 4
+}
+
+
+release=$(get_latest_release ncbi/stxtyper)
+URL=$(get_tarball_url ncbi/stxtyper)
+
+>&2 echo "Downloading StxTyper version $release"
+>&2 echo "Binaries from $URL"
+
+# download and unpack AMRFinder binaries
+    curl --silent -L -O $URL
+    tarball_name=$(echo $URL | perl -pe 's#^.*/(.*)#\1#')
+    tar xfz $tarball_name
+    rm $tarball_name
+    directory=$(echo $tarball_name | sed 's/.tar.gz//')
+    echo $directory

Makefile

@@ -114,7 +114,7 @@ install:
 	then \
 		mkdir -p $(DESTDIR)$(bindir); \
 	fi
-	$(INSTALL) $(BINARIES) $(DATABASE) $(DESTDIR)$(bindir) 
+	$(INSTALL) $(BINARIES) $(DATABASE) test_stxtyper.sh $(DESTDIR)$(bindir) 
 
 # stxtyper binaries for github binary release
 GITHUB_FILE=stxtyper_v$(VERSION_STRING)_$(ARCH)_$(OS)

README.md

@@ -6,39 +6,66 @@ StxTyper is used to determine stx type from nucleotide sequence. Stx (Shiga-toxi
 
 # Installation
 
-## Prerequisites
+## Installing with Bioconda
 
-### C compiler and make
+You'll need Mamba ([Installation instructions](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html)) first.
 
-These generally come standard for unix systems, if not the user will need to intall make
-and GCC. MacOS users will need to go to the [App store and install
-Xcode](https://apps.apple.com/in/app/xcode/id497799835?mt=12). 
+    micromamba create -n stxtyper ncbi-stxtyper \
+      --channel conda-forge \
+      --channel bioconda \
+      --channel defaults \
+      --strict-channel-priority
+
+## Installing from binary
 
-### NCBI BLAST
+### Prerequisites 
 
-StxTyper needs NCBI BLAST binaries in your path (specifically tblastn). If you don't
-already have BLAST installed see https://www.ncbi.nlm.nih.gov/books/NBK569861/
-for instructions to install BLAST binaries.
+#### NCBI BLAST+
 
-Blast can also be installed using bioconda by first installing bioconda, then making sure to activate the environment in which it's installed. 
-- See the [official install miniconda instructions for Linux](https://docs.anaconda.com/free/miniconda/#quick-command-line-install)
-- See the [official install miniconda instructions for MacOS](https://docs.conda.io/en/latest/miniconda.html)
+See below under "Compiling" for instructions to install NCBI BLAST+.
 
-Then run:
+### Download and install Binary
 
-    source ~/miniconda3/bin/activate
-    conda create -y -c conda-forge -c bioconda -n blast blast
-    conda activate blast
+Download the latest binary tarball from https://github.com/ncbi/stxtyper/releases. Untar it and run the tests e.g.:
 
-If you install BLAST via conda in this way you will need to run `conda activate blast` before you can run StxTyper.
+    tar xvfz stxtyper_v*.tar.gz
+    cd stxtyper_v*/
+    ./test_stxtyper.sh
+
+Note that we are currently only publishing binary tarballs for x86 linux.
 
 ## Compiling
 
+### Prerequisites
+
+#### NCBI BLAST+
+
+StxTyper needs NCBI BLAST binaries in your path (specifically tblastn). If you
+don't already have BLAST installed see
+https://www.ncbi.nlm.nih.gov/books/NBK569861/ for the official instructions to
+install BLAST binaries. It's also available in many package repositories, for
+example on Ubuntu:
+
+    sudo apt-get install ncbi-blast+
+
+#### C compiler and make
+
+These are necessary if compiling from source. If using the binary distribution,
+or Bioconda you won't need to worry about these. They generally come standard
+for unix systems, if not the user will need to intall make and GCC. MacOS users
+will need to go to the [App store and install
+Xcode](https://apps.apple.com/in/app/xcode/id497799835?mt=12). 
+
+### Compiling
+
+StxTyper should compile cleanly for Mac and Linux x86 and ARM, though our official policy is we only support x86 Linux.
+
     git clone https://github.com/evolarjun/stxtyper.git
     cd stxtyper
     make
     make test
 
+
 # Usage
 
     stxtyper -n <assembled_nucleotide.fa> [<options>]

test_stxtyper.sh

@@ -16,16 +16,18 @@ FAILURES=0
 TESTS=0
 TEST_TEXT=''
 
+echo "TERM=$TERM"
+
 # some color macros
-if [ "$TERM" != "" ]
+if [ "$TERM" == "" || "$TERM" == "dumb" ]
 then
-    green=`tput setaf 2`  # Set green foreground color (code 2)
-    red=`tput setaf 1`    # Set red foreground color (code 1)
-    reset=`tput sgr0`     # Reset color to default
-else
     green='' # no colors
     red=''
     reset=''
+else
+    green=`tput setaf 2`  # Set green foreground color (code 2)
+    red=`tput setaf 1`    # Set red foreground color (code 1)
+    reset=`tput sgr0`     # Reset color to default
 fi
 
 function test_input_file {