Bump version: 1.2.7-alpha → 1.2.7

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.2.7-alpha
+current_version = 1.2.7
 commit = True
 tag = True
 tag_name = {new_version}

Dockerfile

@@ -1,4 +1,4 @@
-ARG VERSION=1.2.7-alpha
+ARG VERSION=1.2.7
 FROM "predector/predector-base:${VERSION}"
 
 LABEL description="Docker image containing all requirements for the predector pipeline"

README.md

@@ -29,7 +29,7 @@ If you do use results of Predector in your manuscripts please also cite the depe
 Predector ranking does not replace these tools, it is designed to combine information from multiple tools in a useful way.
 We rely heavily on these tools and they should be supported with citations to enable their continued development.
 
-More details on dependencies are available in [the wiki](https://github.com/ccdmb/predector/wiki/1.2.7-alpha#how-should-i-cite-predector) and we provide a [BibTeX](http://www.bibtex.org/Format/) formatted [file with citations](https://github.com/ccdmb/predector/citations.bib), which can be imported into most citation managers.
+More details on dependencies are available in [the wiki](https://github.com/ccdmb/predector/wiki/1.2.7#how-should-i-cite-predector) and we provide a [BibTeX](http://www.bibtex.org/Format/) formatted [file with citations](https://github.com/ccdmb/predector/citations.bib), which can be imported into most citation managers.
 
 
 ## Documentation
@@ -38,12 +38,12 @@ Brief instructions are presented on this page, but extended documentation can be
 
 Quick documentation links:
 
-- [Quick install instructions](https://github.com/ccdmb/predector/wiki/1.2.7-alpha#quick-install)
-- [Extended install instructions](https://github.com/ccdmb/predector/wiki/1.2.7-alpha#extended-dependency-install-guide)
-- [Usage](https://github.com/ccdmb/predector/wiki/1.2.7-alpha#running-the-pipeline)
-- [Description of outputs](https://github.com/ccdmb/predector/wiki/1.2.7-alpha#pipeline-output)
-- [Common issues](https://github.com/ccdmb/predector/wiki/1.2.7-alpha#common-issues)
-- [FAQ](https://github.com/ccdmb/predector/wiki/1.2.7-alpha#faq)
+- [Quick install instructions](https://github.com/ccdmb/predector/wiki/1.2.7#quick-install)
+- [Extended install instructions](https://github.com/ccdmb/predector/wiki/1.2.7#extended-dependency-install-guide)
+- [Usage](https://github.com/ccdmb/predector/wiki/1.2.7#running-the-pipeline)
+- [Description of outputs](https://github.com/ccdmb/predector/wiki/1.2.7#pipeline-output)
+- [Common issues](https://github.com/ccdmb/predector/wiki/1.2.7#common-issues)
+- [FAQ](https://github.com/ccdmb/predector/wiki/1.2.7#faq)
 
 
 If you have any questions, think that some documentation is missing, or have any other suggestions or issues to report, please feel free to create an [issue](https://github.com/ccdmb/predector/issues) or start a [discussion](https://github.com/ccdmb/predector/discussions).
@@ -52,11 +52,11 @@ If you have any questions, think that some documentation is missing, or have any
 ## Install
 
 This is a quick install guide that unfortunately isn't terribly quick.
-For extended documentation and troubleshooting advice, see the [Wiki install documentation](https://github.com/ccdmb/predector/wiki/1.2.7-alpha#quick-install).
+For extended documentation and troubleshooting advice, see the [Wiki install documentation](https://github.com/ccdmb/predector/wiki/1.2.7#quick-install).
 
 **Note that if you have run a previous version of the pipeline, you will need to re-build
 the software environment, as the dependencies may have changed.**
-Please see the [Wiki install documentation](https://github.com/ccdmb/predector/wiki/1.2.7-alpha#optional---remove-previous-software-environments-for-old-versions-of-the-pipeline) for more details.
+Please see the [Wiki install documentation](https://github.com/ccdmb/predector/wiki/1.2.7#optional---remove-previous-software-environments-for-old-versions-of-the-pipeline) for more details.
 
 
 ### Minimal requirements
@@ -122,7 +122,7 @@ For singularity and docker container building you may be prompted for your root
 ```bash
 ENVIRONMENT=docker
 
-curl -s "https://raw.githubusercontent.com/ccdmb/predector/1.2.7-alpha/install.sh" \
+curl -s "https://raw.githubusercontent.com/ccdmb/predector/1.2.7/install.sh" \
 | bash -s "${ENVIRONMENT}" \
     -3 signalp-3.0.Linux.tar.Z \
     -4 signalp-4.1g.Linux.tar.gz \
@@ -134,7 +134,7 @@ curl -s "https://raw.githubusercontent.com/ccdmb/predector/1.2.7-alpha/install.s
     -p phobius101_linux.tar.gz
 ```
 
-This will create the conda environment (named `predector`), or the docker (tagged `predector/predector:1.2.7-alpha`) or singularity (file `./predector.sif`) containers.
+This will create the conda environment (named `predector`), or the docker (tagged `predector/predector:1.2.7`) or singularity (file `./predector.sif`) containers.
 
 **Take note of the message given upon completion**, which will tell you how to use the container or environment with predector.
 
@@ -167,25 +167,25 @@ Use one of the commands below using information given upon completion of depende
 #### Using conda
 
 ```bash
-nextflow run -profile test -with-conda /home/username/path/to/environment -resume -r 1.2.7-alpha ccdmb/predector
+nextflow run -profile test -with-conda /home/username/path/to/environment -resume -r 1.2.7 ccdmb/predector
 ```
 
 #### Using docker
 
 ```bash
-nextflow run -profile test,docker -resume -r 1.2.7-alpha ccdmb/predector
+nextflow run -profile test,docker -resume -r 1.2.7 ccdmb/predector
 
 # if your docker configuration requires sudo use this profile instead
-nextflow run -profile test,docker_sudo -resume -r 1.2.7-alpha ccdmb/predector
+nextflow run -profile test,docker_sudo -resume -r 1.2.7 ccdmb/predector
 ```
 
 #### Using singularity
 
 ```bash
-nextflow run -profile test -with-singularity path/to/predector.sif -resume -r 1.2.7-alpha ccdmb/predector
+nextflow run -profile test -with-singularity path/to/predector.sif -resume -r 1.2.7 ccdmb/predector
 
 # or if you've build the container using docker and it's in your local docker registry.
-nextflow run -profile test,singularity -resume -r 1.2.7-alpha ccdmb/predector
+nextflow run -profile test,singularity -resume -r 1.2.7 ccdmb/predector
 ```
 
 ## Quickstart
@@ -194,25 +194,25 @@ Say you have a set of amino-acid sequences in fasta format in the directory `pro
 The following command will run the complete analysis and the results will be available in a `results` folder.
 
 ```bash
-nextflow run -resume -r 1.2.7-alpha ccdmb/predector --proteome "proteomes/*"
+nextflow run -resume -r 1.2.7 ccdmb/predector --proteome "proteomes/*"
 ```
 
 To improve performance I strongly recommend specifying an appropriate profile for the computer you're running the pipeline on.
-You can find information on available profiles in the [wiki documentation](https://github.com/ccdmb/predector/wiki/1.2.7-alpha#profiles-and-configuration).
+You can find information on available profiles in the [wiki documentation](https://github.com/ccdmb/predector/wiki/1.2.7#profiles-and-configuration).
 
 
 **Please note that if you have previously run a different version of the pipeline on the same computer you will need to ask Nextflow to pull the latest changes.**
-See how to do this in the [extended documentation](https://github.com/ccdmb/predector/wiki/1.2.7-alpha#running-different-pipeline-versions) and the [common issues section](https://github.com/ccdmb/predector/wiki/1.2.7-alpha#common-issues).
+See how to do this in the [extended documentation](https://github.com/ccdmb/predector/wiki/1.2.7#running-different-pipeline-versions) and the [common issues section](https://github.com/ccdmb/predector/wiki/1.2.7#common-issues).
 
 
 ## Outputs
 
 The main output of Predector is a file with the suffix `-ranked.tsv` which is a tab separated values file that can be opened in excel.
 This contains a summarised version of all of the information that you would typically need for evaluating effector protein candidates.
 
-You can find a description of all of the results in [the wiki](https://github.com/ccdmb/predector/wiki/1.2.7-alpha#pipeline-output).
+You can find a description of all of the results in [the wiki](https://github.com/ccdmb/predector/wiki/1.2.7#pipeline-output).
 
-An example set of results is available in the [`test` directory on github](https://github.com/ccdmb/predector/tree/1.2.7-alpha/test/test_set_results).
+An example set of results is available in the [`test` directory on github](https://github.com/ccdmb/predector/tree/1.2.7/test/test_set_results).
 
 
 ## Contributing

base.Dockerfile

@@ -1,7 +1,7 @@
 FROM continuumio/miniconda3:4.11.0
 
 ENV ENVIRONMENT=predector
-ENV VERSION=1.2.7-alpha
+ENV VERSION=1.2.7
 
 LABEL maintainer="[email protected]"
 LABEL description="Docker image containing all non-proprietary requirements for the predector pipeline"

batch_scripts/analyses_slurm_parallel.sh

@@ -7,7 +7,7 @@ export BASENAME=$(dirname ${0})
 
 CONTAINER="${PWD}/predector.sif"
 ANALYSIS=
-PIPELINE_VERSION="1.2.7-alpha"
+PIPELINE_VERSION="1.2.7"
 SOFTWARE_VERSION=
 DATABASE_VERSION=
 FASTA=

docs/install.md

@@ -97,7 +97,7 @@ For singularity and docker container building you may be prompted for your root
 ```bash
 ENVIRONMENT=docker
 
-curl -s "https://raw.githubusercontent.com/ccdmb/predector/1.2.7-alpha/install.sh" \
+curl -s "https://raw.githubusercontent.com/ccdmb/predector/1.2.7/install.sh" \
 | bash -s "${ENVIRONMENT}" \
     -3 signalp-3.0.Linux.tar.Z \
     -4 signalp-4.1g.Linux.tar.gz \
@@ -109,7 +109,7 @@ curl -s "https://raw.githubusercontent.com/ccdmb/predector/1.2.7-alpha/install.s
     -p phobius101_linux.tar.gz
 ```
 
-This will create the conda environment (named `predector`), or the docker (tagged `predector/predector:1.2.7-alpha`) or singularity (file `./predector.sif`) containers.
+This will create the conda environment (named `predector`), or the docker (tagged `predector/predector:1.2.7`) or singularity (file `./predector.sif`) containers.
 
 **Take note of the message given upon completion**, which will tell you how to use the container or environment with Predector.
 
@@ -120,7 +120,7 @@ You can also save the install script locally and run `install.sh --help` to find
 
 ```
 -n|--name         -- For conda, sets the environment name (default: 'predector').
-                     For docker, sets the image tag (default: 'predector/predector:1.2.7-alpha').
+                     For docker, sets the image tag (default: 'predector/predector:1.2.7').
                      For singularity, sets the output image filename (default: './predector.sif').
 -c|--conda-prefix -- If set, use this as the location to store the built conda
                      environment instead of setting a name and using the default
@@ -163,25 +163,25 @@ Use one of the commands below using information given upon completion of depende
 Using conda:
 
 ```bash
-nextflow run -profile test -with-conda /home/username/path/to/environment -resume -r 1.2.7-alpha ccdmb/predector
+nextflow run -profile test -with-conda /home/username/path/to/environment -resume -r 1.2.7 ccdmb/predector
 ```
 
 Using docker:
 
 ```bash
-nextflow run -profile test,docker -resume -r 1.2.7-alpha ccdmb/predector
+nextflow run -profile test,docker -resume -r 1.2.7 ccdmb/predector
 
 # if your docker configuration requires sudo use this profile instead
-nextflow run -profile test,docker_sudo -resume -r 1.2.7-alpha ccdmb/predector
+nextflow run -profile test,docker_sudo -resume -r 1.2.7 ccdmb/predector
 ```
 
 Using singularity:
 
 ```bash
-nextflow run -profile test -with-singularity path/to/predector.sif -resume -r 1.2.7-alpha ccdmb/predector
+nextflow run -profile test -with-singularity path/to/predector.sif -resume -r 1.2.7 ccdmb/predector
 
 # or if you've build the container using docker and it's in your local docker registry.
-nextflow run -profile test,singularity -resume -r 1.2.7-alpha ccdmb/predector
+nextflow run -profile test,singularity -resume -r 1.2.7 ccdmb/predector
 ```
 
 ## Extended dependency install guide
@@ -204,7 +204,7 @@ First we create the conda environment, which includes the non-proprietary depend
 
 ```bash
 # Download the environment config file.
-curl -o environment.yml https://raw.githubusercontent.com/ccdmb/predector/1.2.7-alpha/environment.yml
+curl -o environment.yml https://raw.githubusercontent.com/ccdmb/predector/1.2.7/environment.yml
 
 # Create the environment
 conda env create -f environment.yml
@@ -238,7 +238,7 @@ Modify the source `.tar` archive filenames in the command if necessary.
 Depending on how you installed docker you may need to use `sudo docker` in place of `docker`.
 
 ```bash
-curl -s https://raw.githubusercontent.com/ccdmb/predector/1.2.7-alpha/Dockerfile \
+curl -s https://raw.githubusercontent.com/ccdmb/predector/1.2.7/Dockerfile \
 | docker build \
   --build-arg SIGNALP3=signalp-3.0.Linux.tar.Z \
   --build-arg SIGNALP4=signalp-4.1g.Linux.tar.gz \
@@ -248,12 +248,12 @@ curl -s https://raw.githubusercontent.com/ccdmb/predector/1.2.7-alpha/Dockerfile
   --build-arg PHOBIUS=phobius101_linux.tar.gz \
   --build-arg TMHMM=tmhmm-2.0c.Linux.tar.gz \
   --build-arg DEEPLOC=deeploc-1.0.All.tar.gz \
-  -t predector/predector:1.2.7-alpha \
+  -t predector/predector:1.2.7 \
   -f - \
   .
 ```
 
-Your container should now be available as `predector/predector:1.2.7-alpha` in your docker registry `docker images`.
+Your container should now be available as `predector/predector:1.2.7` in your docker registry `docker images`.
 
 
 ### Building the Singularity container the long way
@@ -279,7 +279,7 @@ export TMHMM=tmhmm-2.0c.Linux.tar.gz
 export DEEPLOC=deeploc-1.0.All.tar.gz
 
 # Download the .def file
-curl -o ./singularity.def https://raw.githubusercontent.com/ccdmb/predector/1.2.7-alpha/singularity.def
+curl -o ./singularity.def https://raw.githubusercontent.com/ccdmb/predector/1.2.7/singularity.def
 
 # Build the .sif singularity image.
 # Note that `sudo -E` is important, it tells sudo to keep the environment variables
@@ -293,7 +293,7 @@ If you've already built the container using docker, you can convert them to sing
 You don't need to use `sudo` even if your docker installation usually requires it.
 
 ```bash
-singularity build predector.sif docker-daemon://predector/predector:1.2.7-alpha
+singularity build predector.sif docker-daemon://predector/predector:1.2.7
 ```
 
 
@@ -323,7 +323,7 @@ Docker containers can be saved as a tarball and copied wherever you like.
 
 ```bash
 # You could pipe this through gzip if you wanted.
-docker save predector/predector:1.2.7-alpha > predector.tar
+docker save predector/predector:1.2.7 > predector.tar
 ```
 
 And on the other end

docs/output.md

@@ -9,7 +9,7 @@ Predector internally removes duplicate sequences at the start to avoid redundant
 The `deduplicated` folder contains the deduplicated sequences, results, and a mapping file of the old ids to new ones.
 
 Other directories will be named after the input filenames and each contains several tables.
-An example set of these results is available in the [`test` directory on github](https://github.com/ccdmb/predector/tree/1.2.7-alpha/test/test_set_results).
+An example set of these results is available in the [`test` directory on github](https://github.com/ccdmb/predector/tree/1.2.7/test/test_set_results).
 
 ### `deduplicated/`
 

docs/running.md

@@ -10,7 +10,7 @@ Conda:
 ```bash
 nextflow run \
   -resume \
-  -r 1.2.7-alpha \
+  -r 1.2.7 \
   -with-conda /path/to/conda/env \
   ccdmb/predector \
   --proteome "my_proteomes/*.faa"
@@ -21,7 +21,7 @@ Docker:
 ```bash
 nextflow run \
   -resume \
-  -r 1.2.7-alpha \
+  -r 1.2.7 \
   -profile docker \
   ccdmb/predector \
   --proteome "my_proteomes/*.faa"
@@ -32,7 +32,7 @@ Singularity:
 ```bash
 nextflow run \
   -resume \
-  -r 1.2.7-alpha \
+  -r 1.2.7 \
   -with-singularity ./path/to/singularity.sif \
   ccdmb/predector \
   --proteome "my_proteomes/*.faa"
@@ -389,7 +389,7 @@ In the config files, you can select these tasks by label.
 
 ### Running different pipeline versions.
 
-We pin the version of the pipeline to run in all of our example commands with the `-r 1.2.7-alpha` parameter.
+We pin the version of the pipeline to run in all of our example commands with the `-r 1.2.7` parameter.
 These flags are optional, but recommended so that you know which version you ran.
 Different versions of the pipelines may output different scores, use different parameters, different output formats etc.
 It also re-enforces the link between the pipeline version and the docker container tags.
@@ -402,7 +402,7 @@ If you have previously run Predector and want to update it to use a new version,
    Likewise, you can run old versions of the pipeline by simply changing `-r`.
 
   ```
-  nextflow run -r 1.2.7-alpha -latest ccdmb/predector --proteomes "my_proteins.fasta"
+  nextflow run -r 1.2.7 -latest ccdmb/predector --proteomes "my_proteins.fasta"
   ```
 
 2. You can ask Nextflow to pull new changes without running the pipeline using `nextflow pull ccdmb/predector`.
@@ -461,12 +461,12 @@ Here's a basic workflow using precomputed results.
 
 
 ```
-nextflow run -profile docker -resume -r 1.2.7-alpha ccdmb/predector \
+nextflow run -profile docker -resume -r 1.2.7 ccdmb/predector \
   --proteome my_old_proteome.fasta
 
 cp -L results/deduplicated/new_results.ldjson ./precomputed.ldjson
 
-nextflow run -profile docker -resume -r 1.2.7-alpha ccdmb/predector \
+nextflow run -profile docker -resume -r 1.2.7 ccdmb/predector \
   --proteome my_new_proteome.fasta --precomputed_ldjson ./precomputed.ldjson
 
 cat results/deduplicated/new_results.ldjson >> ./precomputed.ldjson

install.sh

@@ -8,7 +8,7 @@ REPOBASE="https://raw.githubusercontent.com/ccdmb/predector"
 DOCUMENTATION_URL="https://github.com/ccdmb/predector/wiki"
 
 ### DEFAULT PARAMETERS
-VERSION=1.2.7-alpha
+VERSION=1.2.7
 
 SIGNALP3= #signalp-3.0.Linux.tar.Z
 SIGNALP4= #signalp-4.1g.Linux.tar.gz

nextflow.config

@@ -13,7 +13,7 @@ manifest {
     description = 'A pipeline to predict effectors.'
     mainScript = 'main.nf'
     nextflowVersion = '>=21'
-    version = '1.2.7-alpha'
+    version = '1.2.7'
 }
 
 

singularity.def

@@ -1,9 +1,9 @@
 bootstrap: docker
-From: predector/predector-base:1.2.7-alpha
+From: predector/predector-base:1.2.7
 
 %labels
     Author "[email protected]"
-    Version "1.2.7-alpha"
+    Version "1.2.7"
 
 %help
     A containter will all dependencies for the predector pipeline.