Remove redundant directories

README.org

@@ -1,6 +1,13 @@
 * locigenesis
 
-locigenesis is a tool that generates an immune repertoire and runs it through a sequence reader simulation tool, to generate sequencing errors.
+locigenesis is a tool that generates a human T-cell receptor (TCR), runs it through a sequence reader simulation tool and extracts CDR3.
+
+The goal of this project is to generate both HVR sequences with and without sequencing errors, in order to create datasets for a Machine Learning algorithm.
+
+** Technologies
+
+- [[https://github.com/GreiffLab/immuneSIM/][immuneSIM]]: in silico generation of human and mouse BCR and TCR repertoires
+- [[http://www.pegase-biosciences.com/curesim-a-customized-read-simulator/][CuReSim]]: read simulator that mimics Ion Torrent sequencing
 
 ** Installation
 

docs/notebook.org

@@ -1,46 +0,0 @@
-#+TITLE: locigenesis
-#+AUTHOR: Amin Kasrou Aouam
-#+DATE: 2021-03-10
-* Sequence alignment
-
-Our generated sequences contain the full VJ region, but we are only interested in the CDR3 (Complementarity-determining region). We will proceed by delimiting CDR3, using the known sequences of V and J.
-
-#+begin_src R :results value silent
-v_segments <- readRDS("data/v_segments.rds")
-j_segments <- readRDS("data/j_segments_phe.rds")
-#+end_src
-
-#+begin_src R
-print(v_segments)
-print(j_segments)
-#+end_src
-
-#+RESULTS:
-#+begin_example
-  A DNAStringSet instance of length 147
-      width seq                                             names
-  [1]   326 GATACTGGAATTACCCAGACAC...ATCTCTGCACCAGCAGCCAAGA TRBV1*01_P
-  [2]   326 GATGCTGAAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-1*01_F
-  [3]   326 GATGCTGAAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-1*02_F
-  [4]   326 GATGCTGGAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-2*01_F
-  [5]   326 GATGCTGGAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-2*02_F
-  ...   ... ...
-[143]   324 GATACTGGAGTCTCCCAGAACC...GTATCTCTGTGCCAGCACGTTG TRBV7-9*06_(F)
-[144]   323 .........................TGTATCTCTGTGCCAGCAGCAG TRBV7-9*07_(F)
-[145]   325 GATTCTGGAGTCACACAAACCC...TATTTCTGTGCCAGCAGCGTAG TRBV9*01_F
-[146]   325 GATTCTGGAGTCACACAAACCC...TATTTCTGTGCCAGCAGCGTAG TRBV9*02_F
-[147]   321 GATTCTGGAGTCACACAAACCC...TTTGTATTTCTGTGCCAGCAGC TRBV9*03_(F)
-  A DNAStringSet instance of length 16
-     width seq                                              names
- [1]    32 TGGGCGTCTGGGCGGAGGACTCCTGGTTCTGG                 TRBJ2-2P*01_ORF
- [2]    31 TTTGGAGAGGGAAGTTGGCTCACTGTTGTAG                  TRBJ1-3*01_F
- [3]    31 TTTGGTGATGGGACTCGACTCTCCATCCTAG                  TRBJ1-5*01_F
- [4]    31 TTTGGCAGTGGAACCCAGCTCTCTGTCTTGG                  TRBJ1-4*01_F
- [5]    31 TTCGGTTCGGGGACCAGGTTAACCGTTGTAG                  TRBJ1-2*01_F
- ...   ... ...
-[12]    31 TTTGGCCCAGGCACCCGGCTGACAGTGCTCG                  TRBJ2-3*01_F
-[13]    31 TTCGGGCCAGGCACGCGGCTCCTGGTGCTCG                  TRBJ2-5*01_F
-[14]    31 TTCGGGCCAGGGACACGGCTCACCGTGCTAG                  TRBJ2-1*01_F
-[15]    31 TTCGGGCCGGGCACCAGGCTCACGGTCACAG                  TRBJ2-7*01_F
-[16]    31 GTCGGGCCGGGCACCAGGCTCACGGTCACAG                  TRBJ2-7*02_ORF
-#+end_example

nix/sources.json

@@ -17,10 +17,10 @@
         "homepage": "",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "6f1ce38d0c0b1b25727d86637fd2f3baf7b0f1f6",
-        "sha256": "16da722vqn96k1scls8mr8l909hl66r7y4ik6sad4ms3vmxbkbb3",
+        "rev": "a565a2165ab6e195d7c105a8416b8f4b4d0349a4",
+        "sha256": "1x90qm533lh8xh172rqfcj3pwg8imyx650xgr41rqppmm6fli4w1",
         "type": "tarball",
-        "url": "https://github.com/NixOS/nixpkgs/archive/6f1ce38d0c0b1b25727d86637fd2f3baf7b0f1f6.tar.gz",
+        "url": "https://github.com/NixOS/nixpkgs/archive/a565a2165ab6e195d7c105a8416b8f4b4d0349a4.tar.gz",
         "url_template": "https://github.com/<owner>/<repo>/archive/<rev>.tar.gz"
     }
 }

shell.nix

@@ -21,16 +21,10 @@ let
     installPhase = ''
       mkdir -pv $out/share/java $out/bin
       cp -r ${src} $out/share/java/${name}
-      makeWrapper ${pkgs.jdk}/bin/java $out/bin/CuReSim --add-flags "-jar $out/share/java/${name}/${name}.jar"
+      makeWrapper ${jre}/bin/java $out/bin/CuReSim --add-flags "-jar $out/share/java/${name}/${name}.jar"
     '';
   };
 in mkShell {
-  buildInputs = [
-    R
-    rPackages.immuneSIM
-    rPackages.Biostrings
-    rPackages.stringr
-    jdk
-    CuReSim
-  ];
+  buildInputs =
+    [ R rPackages.immuneSIM rPackages.Biostrings rPackages.stringr CuReSim ];
 }