v0.18.2

build_docs.py

@@ -58,7 +58,7 @@ def get_version(relpath):
 
     for subdir, commands in subdir_and_commands:
         for subcommand in commands:
-            cmd_stub = "bin/singlem {} --full-help-roff |pandoc - -t markdown-multiline_tables-simple_tables-grid_tables -f man |sed 's/\\\\\\[/[/g; s/\\\\\\]/]/g; s/^: //'".format(subcommand)
+            cmd_stub = "singlem {} --full-help-roff |pandoc - -t markdown-multiline_tables-simple_tables-grid_tables -f man |sed 's/\\\\\\[/[/g; s/\\\\\\]/]/g; s/^: //'".format(subcommand)
             man_usage = extern.run(cmd_stub)
 
             subcommand_prelude = 'docs/preludes/{}_prelude.md'.format(subcommand)

docker/build.sh

@@ -5,6 +5,12 @@ export SINGLEM_VERSION=`../bin/singlem --version`
 export SINGLEM_DOCKER_VERSION=wwood/singlem:$SINGLEM_VERSION
 export SINGLEM_DB_BASENAME=`basename $SINGLEM_METAPACKAGE_PATH`
 
+# Check SINGLEM_DB_BASENAME is not an empty string, else croak
+if [ -z "$SINGLEM_DB_BASENAME" ]; then
+    echo "SINGLEM_METAPACKAGE_PATH must be set to the path of the metapackage to use"
+    exit 1
+fi
+
 cp ../singlem.yml . && \
 sed 's/SINGLEM_VERSION/'$SINGLEM_VERSION'/g; s/SINGLEM_DB_BASENAME/'$SINGLEM_DB_BASENAME'/g' Dockerfile.in > Dockerfile && \
 DOCKER_BUILDKIT=1 docker build -t $SINGLEM_DOCKER_VERSION . && \

docs/Installation.md

@@ -9,7 +9,7 @@ if you prefer but we recommend [mamba](https://mamba.readthedocs.io/) for faster
 installation and better error messages.
 
 ```
-mamba create -c bioconda -c conda-forge --name singlem singlem'>='0.18.1
+mamba create -c bioconda -c conda-forge --name singlem singlem'>='0.18.2
 ```
 
 Test if it works by running
@@ -23,45 +23,45 @@ After this, you'll also need to procure the reference data (the "metapackage").
 ## Installation via DockerHub
 A docker image generated from the conda package is [available](https://hub.docker.com/r/wwood/singlem) on DockerHub. After installing Docker, run the following:
 ```
-docker pull wwood/singlem:0.18.1
+docker pull wwood/singlem:0.18.2
 ```
 
 Test if it works by running
 ```
-docker run wwood/singlem:0.18.1 -h
+docker run wwood/singlem:0.18.2 -h
 ```
 
 If the sequence data to be analyzed is in the current working directory, SingleM `pipe` can be used like so:
 ```
-docker run -v `pwd`:`pwd` wwood/singlem:0.18.1 pipe --sequences \
+docker run -v `pwd`:`pwd` wwood/singlem:0.18.2 pipe --sequences \
     `pwd`/my.fastq.gz -p `pwd`/my.profile.csv --threads 4
 ```
 Two things to note:
 
 1. The default SingleM reference data is included in the docker image, so running [singlem data](/tools/data) is not necessary for this installation method - you can jump straight to using `pipe`.
-2. You should not specify `singlem` in the command line, as this is automatic. Simply use e.g. `docker run wwood/singlem:0.18.1 pipe -h`.
+2. You should not specify `singlem` in the command line, as this is automatic. Simply use e.g. `docker run wwood/singlem:0.18.2 pipe -h`.
 
 
 ## Installation via Singularity / Apptainer
 SingleM can be installed via [Singularity](https://sylabs.io/singularity/) or [Apptainer](https://apptainer.org). After installing Singularity or Apptainer, run the following:
 ```
-singularity pull docker://wwood/singlem:0.18.1
+singularity pull docker://wwood/singlem:0.18.2
 ```
 
 Test if it works by running
 ```
-singularity run singlem_0.18.1.sif -h
+singularity run singlem_0.18.2.sif -h
 ```
 
 If the sequence data to be analyzed is in the current working directory, SingleM `pipe` can be used like so:
 ```
-singularity run -B `pwd`:`pwd` singlem_0.18.1.sif pipe --sequences \
+singularity run -B `pwd`:`pwd` singlem_0.18.2.sif pipe --sequences \
     `pwd`/my.fastq.gz -p `pwd`/my.profile.csv --threads 4
 ```
 Two things to note:
 
 1. The default SingleM reference data is included in the docker image, so running [singlem data](/tools/data) is not necessary for this installation method - you can jump straight to using `pipe`.
-2. You should not specify `singlem` in the command line, as this is automatic. Simply use e.g. `singularity run singlem_0.18.1.sif pipe -h`.
+2. You should not specify `singlem` in the command line, as this is automatic. Simply use e.g. `singularity run singlem_0.18.2.sif pipe -h`.
 
 
 ## Installation via PyPI
@@ -82,8 +82,7 @@ git clone https://github.com/wwood/singlem
 cd singlem
 conda env create -n singlem -f singlem.yml
 conda activate singlem
-cd bin
-export PATH=$PWD:$PATH
+pip install -e .
 singlem -h
 ```
 

docs/Installation.md.in

@@ -82,8 +82,7 @@ git clone https://github.com/wwood/singlem
 cd singlem
 conda env create -n singlem -f singlem.yml
 conda activate singlem
-cd bin
-export PATH=$PWD:$PATH
+pip install -e .
 singlem -h
 ```
 

singlem/version.py

@@ -1 +1 @@
-__version__ = "0.18.1"
+__version__ = "0.18.2"