diff --git a/.Rprofile b/.Rprofile
index bb0caed..6c51b55 100644
--- a/.Rprofile
+++ b/.Rprofile
@@ -2,6 +2,13 @@
 ## Options for knitr and Rmarkdown rendering
 ############################################################
 
+if(!"knitr" %in% installed.packages()[,'Package']){
+	install.packages('knitr')
+}
+if(!"rmarkdown" %in% installed.packages()[,'Package']){
+	install.packages('rmarkdown')
+}
+
 library("knitr")
 library("rmarkdown")
 
diff --git a/.gitignore b/.gitignore
index f8fc8c7..d8a3504 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,6 +2,7 @@
 .Rhistory
 .RData
 
+.DS_Store
 
 data/*/*
 !data/process/*
diff --git a/INSTRUCTIONS.md b/INSTRUCTIONS.md
index 2022c4c..c4611f5 100644
--- a/INSTRUCTIONS.md
+++ b/INSTRUCTIONS.md
@@ -16,14 +16,11 @@ the end. You can, but are not obligated to keep the Acknowledgements section.
 You should keep the directory tree
 
 * In the directory tree of the README.md file, customize the comments to fit
-your project. Update this tree as the project proceeds. Replace the word `study`
-in `study.Rmd`, `study.md`, `study.tex`, and `study.pdf` to be the name of your project.
+your project. Update this tree as the project proceeds.
 
-* At the terminal do the following (replacing `LastName_BriefDescription_Journal_Year`
-with the appropriate text...
+* At the terminal do the following to replace the license for the template's repository with the license for your project
 
   ```
-  mv submission/study.Rmd submission/LastName_BriefDescription_Journal_Year.Rmd
   mv newproject_LICENSE.md LICENSE.md
   ```
 
diff --git a/code/get_error.batch b/code/get_error.batch
index 5cba5d0..a18ab76 100644
--- a/code/get_error.batch
+++ b/code/get_error.batch
@@ -1,3 +1,3 @@
 set.current(inputdir=data/mothur, outputdir=data/mothur, processors=8)
-get.groups(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.count_table, fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, taxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy, groups=Mock_S280-Mock2_S366)
+get.groups(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.count_table, fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, taxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy, groups=Mock-Mock2)
 seq.error(fasta=current, count=current, reference=data/references/HMP_MOCK.v4.fasta, aligned=F, processors=8)
diff --git a/code/get_shared_otus.batch b/code/get_shared_otus.batch
index e29334c..457ac2c 100644
--- a/code/get_shared_otus.batch
+++ b/code/get_shared_otus.batch
@@ -1,6 +1,6 @@
 set.dir(input=data/mothur, output=data/mothur, seed=19760620)
 set.current(processors=8)
-remove.groups(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.count_table, fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, taxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy, groups=Mock_S280-Mock2_S366)
+remove.groups(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.count_table, fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, taxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy, groups=Mock-Mock2)
 dist.seqs(fasta=current, cutoff=0.03)
 cluster(column=current, count=current)
 make.shared(list=current, count=current, label=0.03)
diff --git a/submission/study.Rmd b/submission/manuscript.Rmd
similarity index 100%
rename from submission/study.Rmd
rename to submission/manuscript.Rmd
diff --git a/submission/study.md b/submission/manuscript.md
similarity index 100%
rename from submission/study.md
rename to submission/manuscript.md
diff --git a/submission/study.pdf b/submission/manuscript.pdf
similarity index 100%
rename from submission/study.pdf
rename to submission/manuscript.pdf
diff --git a/submission/study.tex b/submission/manuscript.tex
similarity index 100%
rename from submission/study.tex
rename to submission/manuscript.tex