Merge pull request #28 from cnobles/report_temp

Update to v0.9.4

.circleci/config.yml

@@ -15,12 +15,12 @@ jobs:
       # Download and cache dependencies
       - restore_cache:
           keys:
-          - v1-dependencies-{{ checksum "etc/build.v0.9.0.yml" }}
+          - v1-dependencies-{{ checksum "etc/build.v0.9.2.txt" }}
 
       - run:
           name: install
           command: |
-            bash install.sh
+            bash install.sh -v
 
       - run:
           name: run tests
@@ -30,4 +30,4 @@ jobs:
       - save_cache:
           paths:
             - ~/miniconda3
-          key: v1-dependencies-{{ checksum "etc/build.v0.9.0.yml" }}
+          key: v1-dependencies-{{ checksum "etc/build.v0.9.2.txt" }}

.gitignore

@@ -5,6 +5,7 @@
 .Ruserdata
 *.RData
 *.Rproj
+*.Rmd
 .snakemake
 output
 *.yml

.version

@@ -1 +1 @@
-v0.9.3
+v0.9.4

README.md

@@ -8,7 +8,7 @@
 Bioinformatic pipeline for processing iGUIDE and GUIDE-seq samples.
 
 ### Description
-iGUIDE is a pipeline written in [snakemake](http://snakemake.readthedocs.io/) for processing and analyzing double-strand DNA break events. These events may be induced, such as by designer nucleases like Cas9, or spontaneous, as produced through DNA replication or ionizing radiation. A laboratory bench-side protocol accompanies this software pipeline, and can be found XXX. 
+iGUIDE is a pipeline written in [snakemake](http://snakemake.readthedocs.io/) for processing and analyzing double-strand DNA break events. These events may be induced, such as by designer nucleases like Cas9, or spontaneous, as produced through DNA replication or ionizing radiation. A laboratory bench-side protocol accompanies this software pipeline, and can be found [**https://doi.org/10.1186/s13059-019-1625-3**](https://doi.org/10.1186/s13059-019-1625-3). 
 
 Below, this readme gives the reader a overview of the pipeline, including how to install and process a sample dataset. Processing a sample data set is broken into three parts: 
 
@@ -35,44 +35,71 @@ bash install.sh
 
 cd path/to/iGUIDE
 bash install.sh -e {env_name}
+
+# Or include simulation test
+cd path/to/iGUIDE
+bash install.sh -t
+
+# For help with install options:
+cd path/to/iGUIDE
+bash install.sh -h
 ```
 
 ### An Example Run
-To perform a local test of running the iGUIDE informatic pipeline, run the below code after installing. This block first activates your conda environment, 'iguide' by default, and then creates a test directory within the analysis directory. The run information is stored in the run specific configuration file (config file). Using the '-np' flag with the snakemake call will perform a dry-run (won't actually process anything) and print the commands to the terminal, so you can see what snakemake is about to perform. Next, the test data is moved to the input directory underneath the new test run directory. Then the entirety of processing can start. Using the '--dag' flag and piping the output to 'dot -Tsvg' will generate a vector graphic of the directed acyclic graph (dag) workflow that snakemake will follow given the data provided. 
+To perform a local test of running the iGUIDE informatic pipeline, run the below code after installing. This block first activates your conda environment, 'iguide' by default, and then creates a test directory within the analysis directory. The run information is stored in the run specific configuration file (config file). Using the '-np' flag with the snakemake call will perform a dry-run (won't actually process anything) and print the commands to the terminal, so you can see what snakemake is about to perform. Next, the test data can be moved to the input directory underneath the new test run directory or the path to the input data needs to be included in the config file. Then the entirety of processing can start. 
 
 ```
 # If conda is not in your path ...
-PREFIX=${HOME}/miniconda3
-export PATH=${PATH}:${PREFIX}/bin
+source ${HOME}/miniconda3/etc/profile.d/conda.sh
 
 # Activate iguide environment
 conda activate iguide
 
-# Check the setup workflow
-iguide setup configs/simulation.config.yml -- -np
+# After constructing the config file and having reference files (i.e. sampleinfo)
+# You can check the samples associated with the run.
+iguide list_samples configs/simulation.config.yml
 
 # Create test analysis directory
+# (The simulation configuration file is used by default and does not need to be specified)
+iguide setup configs/simulation.config.yml -- -np
 iguide setup configs/simulation.config.yml
 
-# Check the run workflow
+# Process a simulation dataset
 iguide run configs/simulation.config.yml -- -np
+iguide run configs/simulation.config.yml -- --latency-wait 30
+cat analysis/simulation/output/unique_sites.simulation.csv
 
-# Generate test DAG graph
-iguide run configs/simulation.config.yml -- --dag | dot -Tsvg > \
-    analysis/simulation/reports/simulation.dag.svg
+# After run completion, generate a report in a different format than standard
+iguide report analysis/simulation/output/edited_sites.simulation.rds \
+  -c configs/simulation.config.yml \
+  -o analysis/simulation/reports/report.simulation.pdf \
+  -s sampleInfo/simulation.supp.csv \
+  -t pdf
 
-# Run iGUIDE to analyze simulation dataset
-iguide run configs/simulation.config.yml -- --latency-wait 30
+# When you are all finished and ready to archive / remove excess files, a minimal configuration
+# can be achived with the 'clean' subcommand.
+iguide clean configs/simulation.config.yml
 
-# Output some of the analysis data to check.
-cat analysis/simulation/output/unique_sites.simulation.csv
+# Or you realized you messed up all the input and need to restart
+iguide clean configs/simulation.config.yml --remove_proj
 
 # Deactivate the environment
 conda deactivate
 ```
 
 ### Changelog:
 
+**v0.9.4 (January 30th, 2019)**
+
+* Updated 'report' utility and formating
+  + custom templates now accepted
+  + included as subcommand, check with 'iguide report -h'
+  + pdf and html options report 'nicely' even when printed from either
+* Updated build to v0.9.2 to support new formating in report
+* Builds are constructed from spec files rather than yaml requirements
+* Included the 'clean' subcommand to reduce size of processed projects
+  + after cleaning a project, only terminal data files will remain
+
 **v0.9.3 (January 11th, 2019)**
 
 * Added 'list_samples' subcommand to list samples within a project.

docs/index.rst

@@ -6,15 +6,14 @@
 Welcome to iGUIDE's documentation
 ==================================
 
-===========
 Description
 ===========
 
 Software pipeline for processing and analyzing double-strand DNA break events. 
 These events may be induced, such as by designer nucleases like Cas9, or 
 spontaneous, as produced through DNA replication or ionizing radiation. A 
 laboratory bench-side protocol accompanies this software pipeline, and can be 
-found XXX. 
+found (https://doi.org/10.1186/s13059-019-1625-3). 
 
 This documentation gives the reader an overview of the pipeline, including
 how to install and process a sample dataset. Processing a sample data set is 

docs/pages/quickstart.rst

@@ -108,22 +108,36 @@ directory. The run information is stored in the run specific configuration file
 dry-run (won't actually process anything) and print the commands to the 
 terminal, so you can see what snakemake is about to perform. Next, the test data 
 is moved to the input directory underneath the new test run directory. Then the 
-entirety of processing can start. Using the ``--dag`` flag and piping the output 
-to ``dot -Tsvg`` will generate a vector graphic of the directed acyclic graph 
-(dag) workflow that snakemake will follow given the data provided::
+entirety of processing can start.::
 
+  # After constructing the config file and having reference files (i.e. sampleinfo)
+  # You can check the samples associated with the run.
+  iguide list_samples configs/simulation.config.yml
 
   # Create test analysis directory
   # (The simulation configuration file is used by default and does not need to be specified)
   iguide setup configs/simulation.config.yml -- -np
   iguide setup configs/simulation.config.yml
 
-  # Generate test DAG graph
+  # Process a simulation dataset
   iguide run configs/simulation.config.yml -- -np
-  iguide run configs/simulation.config.yml -- --dag | dot -Tsvg > analysis/simulation/reports/simulation.dag.svg
   iguide run configs/simulation.config.yml -- --latency-wait 30
   cat analysis/simulation/output/unique_sites.simulation.csv
 
+  # After run completion, generate a report in a different format than standard
+  iguide report analysis/simulation/output/edited_sites.simulation.rds \
+    -c configs/simulation.config.yml \
+    -o analysis/simulation/reports/report.simulation.pdf \
+    -s sampleInfo/simulation.supp.csv \
+    -t pdf
+
+  # When you are all finished and ready to archive / remove excess files, a minimal configuration
+  # can be achived with the 'clean' subcommand.
+  iguide clean configs/simulation.config.yml
+
+  # Or you realized you messed up all the input and need to restart
+  iguide clean configs/simulation.config.yml --remove_proj
+
 
 Uninstall
 ---------