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Use internal functions more consistently

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mjsteinbaugh committed Aug 18, 2019
1 parent 4f40177 commit 1185a9c192a408ea8b193c3bd3b5f5573b6068a0
Showing with 204 additions and 219 deletions.
  1. +1 −1 bin/autopad-samples
  2. +1 −1 bin/copy-bam-files
  3. +1 −1 bin/delete-file-system-cruft
  4. +1 −1 bin/delete-named-subdirs
  5. +1 −1 bin/docker-run-image
  6. +1 −1 bin/dotfile
  7. +1 −1 bin/extract-fastq
  8. +1 −1 bin/fastq-dump-from-sra-list
  9. +1 −1 bin/fastq-lanepool
  10. +1 −1 bin/fastq-reads-per-file
  11. +1 −1 bin/ffmpeg-alac-to-flac
  12. +1 −1 bin/ffmpeg-flac-to-alac
  13. +1 −1 bin/find-and-replace
  14. +1 −1 bin/find-build-cellar-symlinks
  15. +1 −1 bin/ftp-mirror
  16. +1 −1 bin/git-pull-recursive
  17. +1 −1 bin/git-push-recursive
  18. +1 −1 bin/git-push-submodules
  19. +1 −1 bin/git-reset-fork-to-upstream
  20. +1 −1 bin/git-status-recursive
  21. +1 −1 bin/gzip-dir
  22. +1 −1 bin/indrops-bcl2fastq
  23. +1 −1 bin/indrops-i5-sample-index-counts
  24. +1 −1 bin/install-anaconda3
  25. +1 −1 bin/install-conda-env-pandoc
  26. +1 −1 bin/install-conda-env-texlive-core
  27. +1 −1 bin/install-doom-emacs
  28. +1 −1 bin/install-dotfiles
  29. +1 −1 bin/install-ensembl-api
  30. +1 −1 bin/install-miniconda3
  31. +1 −1 bin/install-perlbrew
  32. +1 −1 bin/install-perlbrew-perl
  33. +1 −1 bin/install-perlbrew-system
  34. +1 −1 bin/install-python-virtualenv
  35. +1 −1 bin/install-python-virtualenv-reticulate
  36. +1 −1 bin/install-rbenv
  37. +1 −1 bin/install-rbenv-ruby
  38. +1 −1 bin/install-rcheck
  39. +1 −1 bin/install-spacemacs
  40. +1 −1 bin/ip-address
  41. +4 −28 bin/koopa
  42. +1 −1 bin/link-cellar
  43. +1 −1 bin/list-dotfiles
  44. +1 −1 bin/list-path-priority
  45. +1 −1 bin/md5sum-check-to-new-md5-file
  46. +1 −1 bin/move-files-up-1-level
  47. +1 −1 bin/move-into-dated-dirs-by-filename
  48. +1 −1 bin/move-into-dated-dirs-by-timestamp
  49. +1 −1 bin/nfiletypes
  50. +1 −1 bin/r-javareconf
  51. +1 −1 bin/rename-fq-to-fastq
  52. +1 −1 bin/rename-from-csv
  53. +1 −1 bin/reset-permissions
  54. +1 −1 bin/sort-lines
  55. +1 −1 bin/sox-downsample
  56. +1 −1 bin/today-bucket
  57. +1 −1 bin/trash
  58. +1 −1 bin/update-conda
  59. +1 −1 bin/update-tex
  60. +1 −1 bin/wget-recursive
  61. +1 −1 bin/youtube-mp3
  62. +1 −1 bin/youtube-thumbnail
  63. +1 −1 host/azure/bin/rsync-azure-files
  64. +1 −1 host/azure/include/header.sh
  65. +1 −1 host/azure/sbin/bcbio-admin-clean-anaconda-pkgs
  66. +1 −1 host/azure/sbin/bcbio-admin-find-broken-links
  67. +1 −1 host/azure/sbin/bcbio-admin-rsync-cpi
  68. +1 −1 host/azure/sbin/bcbio-admin-run-tests
  69. +1 −1 host/azure/sbin/bcbio-admin-symlinks
  70. +1 −1 host/azure/sbin/install-azure-base
  71. +1 −1 host/azure/sbin/install-azure-cli
  72. +1 −1 host/azure/sbin/symlink-docker
  73. +1 −1 host/azure/sbin/update-r-site-library
  74. +1 −1 host/harvard-o2/bin/load-r-3.5.1
  75. +1 −1 host/harvard-o2/bin/srun-interactive-16gb-6hr
  76. +1 −1 host/harvard-o2/bin/srun-interactive-1gb-1hr
  77. +1 −1 host/harvard-o2/bin/srun-interactive-8gb-6hr-x11
  78. +1 −1 host/harvard-o2/include/header.sh
  79. +1 −1 host/harvard-odyssey/bin/srun-interactive-1gb-1hr
  80. +1 −1 host/harvard-odyssey/include/header.sh
  81. +1 −1 os/amzn/include/header.sh
  82. +1 −1 os/amzn/sbin/install-amzn-base
  83. +1 −1 os/darwin/bin/brew-cleanup
  84. +1 −1 os/darwin/bin/brew-status
  85. +1 −1 os/darwin/bin/brew-upgrade
  86. +1 −1 os/darwin/bin/convert-utf8-nfd-to-nfc
  87. +1 −1 os/darwin/bin/create-dmg
  88. +1 −1 os/darwin/bin/delete-adobe-bridge-cache
  89. +1 −1 os/darwin/bin/dotfile-icloud
  90. +1 −1 os/darwin/bin/gh-pages
  91. +1 −1 os/darwin/bin/install-cellar-openssl
  92. +1 −1 os/darwin/bin/install-homebrew
  93. +1 −1 os/darwin/bin/install-homebrew-recommended-recipes
  94. +1 −1 os/darwin/bin/open-app
  95. +1 −1 os/darwin/bin/update-defaults
  96. +1 −1 os/darwin/include/header.sh
  97. +1 −1 os/darwin/sbin/brew-cask-quarantine-fix
  98. +1 −1 os/darwin/sbin/dropbox-symlinks
  99. +1 −1 os/darwin/sbin/flush-dns
  100. +1 −1 os/darwin/sbin/install-r-devel
  101. +1 −1 os/darwin/sbin/sudo-open-app
  102. +1 −1 os/darwin/sbin/uninstall-adobe
  103. +1 −1 os/debian/bin/install-cellar-bash
  104. +1 −1 os/debian/bin/install-cellar-coreutils
  105. +1 −1 os/debian/bin/install-cellar-emacs
  106. +1 −1 os/debian/bin/install-cellar-htop
  107. +1 −1 os/debian/bin/install-cellar-python
  108. +1 −1 os/debian/bin/install-cellar-tmux
  109. +1 −1 os/debian/bin/install-cellar-vim
  110. +1 −1 os/debian/bin/install-cellar-zsh
  111. +1 −1 os/debian/include/header.sh
  112. +1 −1 os/debian/sbin/install-debian-base
  113. +1 −1 os/debian/sbin/install-git-lfs
  114. +1 −1 os/debian/sbin/install-oracle-java-12
  115. +1 −1 os/debian/sbin/install-pandoc
  116. +1 −1 os/debian/sbin/install-perl-rename
  117. +1 −1 os/debian/sbin/install-rstudio-server
  118. +1 −1 os/debian/sbin/update-debian
  119. +2 −2 os/fedora/bin/install-cellar-bash
  120. +2 −2 os/fedora/bin/install-cellar-coreutils
  121. +2 −2 os/fedora/bin/install-cellar-emacs
  122. +2 −2 os/fedora/bin/install-cellar-gdal
  123. +2 −2 os/fedora/bin/install-cellar-git
  124. +2 −2 os/fedora/bin/install-cellar-gnupg
  125. +2 −2 os/fedora/bin/install-cellar-gsl
  126. +1 −1 os/fedora/bin/install-cellar-hdf5
  127. +1 −1 os/fedora/bin/install-cellar-htop
  128. +2 −2 os/fedora/bin/install-cellar-openssl
  129. +2 −2 os/fedora/bin/install-cellar-proj
  130. +2 −2 os/fedora/bin/install-cellar-python
  131. +2 −2 os/fedora/bin/install-cellar-r
  132. +2 −2 os/fedora/bin/install-cellar-tmux
  133. +2 −2 os/fedora/bin/install-cellar-vim
  134. +2 −2 os/fedora/bin/install-cellar-zsh
  135. +1 −1 os/fedora/include/header.sh
  136. +2 −2 os/fedora/sbin/enable-epel-7
  137. +2 −2 os/fedora/sbin/install-docker-ce
  138. +2 −2 os/fedora/sbin/install-fedora-base
  139. +1 −1 os/fedora/sbin/install-perl-rename
  140. +1 −1 os/fedora/sbin/install-rstudio-server
  141. +1 −1 os/fedora/sbin/install-shiny-server
  142. +1 −1 os/fedora/sbin/update-fedora
  143. +1 −1 os/linux/bin/git-clone-cloudbiolinux
  144. +1 −1 os/linux/bin/install-bcbio
  145. +1 −1 os/linux/bin/install-bcbio-ensembl-genome
  146. +1 −1 os/linux/bin/install-bcbio-genomes
  147. +1 −1 os/linux/bin/install-cellar-genrich
  148. +1 −1 os/linux/bin/install-cellar-shellcheck
  149. +1 −1 os/linux/bin/install-haskell-stack
  150. +1 −1 os/linux/bin/patch-bcbio
  151. +1 −1 os/linux/bin/upgrade-bcbio
  152. +1 −1 os/linux/include/header.sh
  153. +1 −1 os/linux/sbin/install-bcbio-vm
  154. +1 −1 os/ubuntu/include/header.sh
  155. +1 −1 os/ubuntu/sbin/install-r-cran
  156. +1 −1 sbin/install-tex-packages
  157. +1 −1 sbin/link-coreutils-env
  158. +1 −1 shell/zsh/bin/install-oh-my-zsh
  159. +1 −1 shell/zsh/bin/install-zsh-autosuggestions
  160. +2 −2 system/activate/exports/path.sh
  161. +1 −1 system/activate/programs/bcbio.sh
  162. +1 −1 system/include/functions/b.sh
  163. +9 −3 system/include/functions/h.sh
  164. +2 −1 system/include/functions/l.sh
  165. +2 −0 system/include/functions/o.sh
  166. +1 −1 system/include/functions/u.sh
  167. +1 −1 system/include/koopa/info.sh
  168. +1 −1 system/include/koopa/list.R
  169. +1 −1 system/include/koopa/update.sh
  170. +3 −3 system/install/dotfiles-local.sh
  171. +1 −1 uninstall
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Autopad sample file names that begin with a number.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Copy BAM and BAI index sidecar files to a destination.
# Updated 2019-06-26.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Remove file system cruft.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Remove named subdirectories.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Run Docker image locally.
# Updated 2019-07-25.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Symlink dot file.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Extract FASTQs files inside a TAR file.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# FASTQ dump from Sequence Read Archive (SRA) accession list.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Pool lane-split FASTQ files.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Get the number of reads per FASTQ file.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Use ffmpeg to transcode ALAC (Apple Lossless) to FLAC.
# Updated 2019-07-28.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Use ffmpeg to transcode FLAC to ALAC (Apple Lossless).
# Updated 2019-07-28.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Global find and replace in files using sed.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Find build cellar symbolic links.
# Updated 2019-06-26.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Recursively download (mirror) over FTP using wget.
# Updated 2019-07-30.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Pull all git repositories recursively.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Push all repositories recursively.
# Updated 2019-06-25.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Update and commit submodules.
# Updated 2019-06-25.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Reset fork to upstream.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Get the status of all git repositories.
# Updated 2019-06-25.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Create a gzipped tar file from current working directory.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Generate FASTQ files from inDrops Illumina BCL data.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# inDrops sample barcode counts from i5 indexes.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Install Anaconda.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Install conda pandoc.
# Updated 2019-06-25.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Install conda TeX Live.
# Updated 2019-06-25.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Install Doom Emacs.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Install dot files.
# Updated 2019-08-14.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Install Ensembl API.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Install Miniconda.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Install Perlbrew.
# Updated 2019-06-25.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Install recommended Perl release via perlbrew.
# Updated 2019-08-15.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Install Perlbrew system Perl.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Set up python virtual environment.
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Install reticulate Python virtual environment.
# Updated 2019-08-14.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Install Ruby environment manager (rbenv).
# Updated 2019-06-23.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Install recommended Ruby release via rbenv.
# Updated 2019-06-24.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Install Rcheck scripts for R package locally.
# Updated 2019-07-31.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# Install spacemacs.
# Updated 2019-06-25.
@@ -2,7 +2,7 @@
set -Eeu -o pipefail

# shellcheck source=/dev/null
source "$(koopa header bash)"
source "$(_koopa_header bash)"

# IP address.
# Updated 2019-06-23.

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