Fixe some issues, when I try to run it frome scratch.

README.md

@@ -8,6 +8,7 @@ The repository at https://github.com/pachterlab/sleuth_paper_analysis should alw
 # Preliminaries
 
 - Install [snakemake](https://bitbucket.org/johanneskoester/snakemake)
+- Install [sratoolkit](https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software)
 - Download and install `R` along with dependencies listed below (R dependencies section)
 - Updated the `BASE` variable in `config.py` to represent the base path on your system
 
@@ -36,6 +37,8 @@ Install using `install.packages()`
 - `jsonlite`
 - `reshape2`
 - `scales`
+- `VennDiagram`
+- `knitr`
 
 ### from Bioconductor
 

annotation/Snakefile

@@ -36,7 +36,7 @@ rule get_genome:
     output:
         GENOME_FA
     shell:
-        'curl -o {output}'
+        'curl -o {output}.gz'
         ' --silent'
         ' ftp://ftp.ensembl.org/pub/release-80/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz'
         ' && '

bottomly/R/fdr.Rmd

@@ -86,6 +86,7 @@ p
 ```
 
 ```{r}
+dir.create(base_dir, showWarnings = FALSE, recursive=T)
 filename <- file.path(base_dir, paste0('isoform_resampling', default_extension))
 save_plot(filename, p, base_aspect_ratio = 0.75, base_height = 15)
 ```

bottomly/R/var_plots.Rmd

@@ -372,6 +372,7 @@ p
 ```
 
 ```{r}
+dir.create(base_dir, showWarnings = FALSE, recursive=T)
 filename <- file.path(base_dir, paste0('inferential_variance',
   default_extension))
 save_plot(filename, p, base_aspect_ratio = 1.6, base_height = 15)

bottomly/Snakefile

@@ -190,6 +190,8 @@ rule run_benchmarks_isoform:
     input:
         expand('results/single/{id}/kallisto/abundance.h5', id = SRA_SINGLE),
         expand('results/validation/{num}/cuffdiff/isoform_exp.diff',
+            num = range(1, 20 + 1)),
+        expand('results/training/{num}/cuffdiff/gene_exp.diff',
             num = range(1, 20 + 1))
     output:
         'results/isoform_self_benchmark.rds',
@@ -234,6 +236,7 @@ def get_cuffdiff_training(wildcards):
     b = TRAINING_B[num].split(' ')
     ids = a + b
     return expand('results/single/{id}/cuffquant/abundances.cxb', id = ids)
+
 rule cuffdiff_training:
     input:
         get_cuffdiff_training
@@ -269,6 +272,7 @@ def get_cuffdiff_validation(wildcards):
     b = VALIDATION_B[num].split(' ')
     ids = a + b
     return expand('results/single/{id}/cuffquant/abundances.cxb', id = ids)
+
 rule cuffdiff_validation:
     input:
         get_cuffdiff_validation

cuffdiff2_analysis/R/investigating_variance.Rmd

@@ -20,8 +20,9 @@ source('../../geuvadis/R/benchmark_methods.R')
 source('../../simulation_core/R/simulate_de.R')
 
 library('sleuth')
+info_save = info
 
-info <- dplyr::mutate(info,
+info <- dplyr::mutate(info_save,
   condition = ifelse(condition == 'scramble', 'A', 'B'))
 
 sir <- run_sleuth(info, max_bootstrap = 100)
@@ -121,7 +122,7 @@ ggplot()
 ## comparing results to limma and DESeq2
 
 ```{r}
-info <- dplyr::mutate(info,
+info <- dplyr::mutate(info_save,
   condition = ifelse(condition == 'scramble', 'A', 'B'))
 
 sgr <- run_sleuth(info, max_bootstrap = 30, gene_column = 'ens_gene',
@@ -156,6 +157,7 @@ fp_plots <- lapply(fp_in_order[1:9],
 
 
 ```{r}
+library(cowplot)
 plot_grid(plotlist = fp_plots)
 ```
 

cuffdiff2_analysis/Snakefile

@@ -29,15 +29,13 @@ rule all:
 
 rule metadata:
     output:
-        META,
-        "metadata/hiseq_accession.txt"
+        META
     shell:
         source_r('R', 'get_sample_info.R')
 
 rule fastq_dump_paired:
     input:
-        META,
-        "metadata/hiseq_accession.txt"
+        META
     output:
         'data/paired/{id}',
         'data/paired/{id}/{id}_1.fastq.gz',

software/Snakefile

@@ -141,9 +141,9 @@ rule get_seqtk:
         branch = '4feb6e81444ab6bc44139dd3a125068f81ae4ad8'
     shell:
         'git clone {params.url} {params.tmp};'
+        ' cd {params.tmp};'
         ' git reset --hard {params.branch};'
         # 'git clone --branch {params.branch} --depth 1 {params.url} {params.tmp};'
-        ' cd {params.tmp};'
         ' make;'
         ' cd ..;'
         # 'find {params.tmp} -maxdepth 1 -perm +o+x -type f -exec cp {{}} bin \;'
@@ -160,8 +160,8 @@ rule get_BitSeq:
         branch = '72fe9d9408467ac55fcbc717472e45ec71626b45'
     shell:
         'git clone {params.url} {params.tmp};'
-        ' git reset --hard {params.branch};'
         ' cd {params.tmp};'
+        ' git reset --hard {params.branch};'
         ' make;'
         ' cd ..;'
         # 'find {params.tmp} -maxdepth 1 -perm +o+x -type f -exec cp {{}} bin \;'