Updates report (#15)

* changes to address count bug * updates report and its dependencies
pnnl · Jul 17, 2018 · 982a0b2 · 982a0b2
1 parent 0156425
commit 982a0b2
Show file tree

Hide file tree

Showing 15 changed files with 804 additions and 742 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,7 @@
 example/annotation_references
 example/mothur_sop_results
 example/example_its_results
+example/additional_data
 .snakemake
 
 # Byte-compiled / optimized / DLL files

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,2 +1,3 @@
 include hundo/Snakefile
 include hundo/environment.yml
+include hundo/scripts/build_report.py
diff --git a/README.md b/README.md
@@ -27,10 +27,8 @@ https://bioconda.github.io/#using-bioconda
 Really, you just need to make sure `conda` is executable and you've set up your channels (numbers 1 and 2). Then:
 
 ```
-conda install python=3.6 \
-    pyyaml snakemake>=5.1.4 biopython \
-    biom-format=2.1.6 numpy pandas=0.23.1 \
-    plotly=2.7.0
+conda install python>=3.6 click \
+    pyyaml snakemake>=5.1.4 biopython
 pip install hundo
 ```
 

diff --git a/README.rst b/README.rst
@@ -34,10 +34,8 @@ set up your channels (numbers 1 and 2). Then:
 
 ::
 
-    conda install python=3.6 \
-        pyyaml snakemake>=5.1.4 biopython \
-        biom-format=2.1.6 numpy pandas=0.23.1 \
-        plotly=2.7.0
+    conda install python>=3.6 click \
+        pyyaml snakemake>=5.1.4 biopython
     pip install hundo
 
 

diff --git a/docs/install.rst b/docs/install.rst
@@ -11,10 +11,8 @@ set up your channels (steps 1 and 2). Then:
 
 ::
 
-    conda install python=3.6 \
-        pyyaml snakemake>=5.1.4 biopython \
-        biom-format=2.1.6 numpy pandas=0.23.1 \
-        plotly=2.7.0
+    conda install python>=3.6 click \
+        pyyaml snakemake>=5.1.4 biopython
     pip install hundo
 
 To update to the newest version of Hundo, run
@@ -26,10 +24,8 @@ To update to the newest version of Hundo, run
 Alternatively, if you do not want any new executables in your environment
 you can install into a new conda environment, e.g. hundo_env::
 
-    conda create --name hundo_env python=3.6 \
-        pyyaml snakemake>=5.1.4 biopython \
-        biom-format=2.1.6 numpy pandas=0.23.1 \
-        plotly=2.7.0
+    conda create --name hundo_env python>=3.6 \
+        click pyyaml snakemake>=5.1.4 biopython
     source activate hundo_env
     pip install hundo
 

diff --git a/example/log.txt b/example/log.txt
diff --git a/example/mothur_sop_data/Sample1_R1.fastq b/example/mothur_sop_data/Sample1_R1.fastq
diff --git a/example/mothur_sop_data/Sample1_R1.fastq.gz b/example/mothur_sop_data/Sample1_R1.fastq.gz
diff --git a/example/mothur_sop_data/Sample1_R2.fastq b/example/mothur_sop_data/Sample1_R2.fastq
diff --git a/example/mothur_sop_data/Sample1_R2.fastq.gz b/example/mothur_sop_data/Sample1_R2.fastq.gz