ADD: split_paf

.gitignore

@@ -22,3 +22,5 @@ build
 *.fq
 *.fq.index
 edit.*
+Makefile
+.vscode

README.md

@@ -67,5 +67,5 @@ The princple is that 3rd party libraries and their derivatives
 are basically licensed under their original licenses, while
 what we developed from scratch are licensed under the modified BSD.
 The 3rd party libraries include SQLite3 (http://www.sqlite.org/), sqdbcpp
-(http://code.google.com/p/sqdbcpp/).
+(http://code.google.com/p/sqdbcpp/), imgcat2 (modified from imgcat, https://iterm2.com/3.2/documentation-images.html).
 

conda/before_build.sh

@@ -0,0 +1,35 @@
+
+if [[ ! -n CONDA_EXE ]]; then
+    echo "ERROR: This script must be executed from a conda environment."
+    exit 2
+fi
+
+# Make sure that this script is sourced.
+# See https://stackoverflow.com/questions/2683279/how-to-detect-if-a-script-is-being-sourced for details.
+is_sourced() {
+    if [ -n "$ZSH_VERSION" ]; then
+        case $ZSH_EVAL_CONTEXT in *:file:*) return 0;; esac
+    else  # Add additional POSIX-compatible shell names here, if needed.
+        case ${0##*/} in dash|bash|ksh|sh) return 0;; esac
+    fi
+    return 1
+}
+
+if is_sourced ; then
+    module unload gcc
+    unset CFLAGS
+    unset CPPFLAGS
+    unset CXXFLAGS
+    unset LDFLAGS
+    unset FCFLAGS
+    unset JAVA_HOME
+    unset FC
+    export CONDA_BUILD=1
+    conda activate build
+    unset FC
+    export CPPFLAGS="-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /include"
+    export CFLAGS="-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix"
+    export LDFLAGS="-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/lib -Wl,-rpath-link,/lib -L/lib"
+else
+    echo "ERROR: This script must be sourced."
+fi

conda/glow/1.4.1/build.sh

@@ -0,0 +1,4 @@
+
+
+mkdir -p ${PREFIX}/bin/
+cp glow ${PREFIX}/bin/

conda/glow/1.4.1/meta.yaml

@@ -0,0 +1,15 @@
+{% set version = "1.4.1" %}
+
+package:
+  name: glow
+  version: {{ version }}
+
+source:
+  url: https://github.com/charmbracelet/glow/releases/download/v{{ version }}/glow_{{ version }}_linux_x86_64.tar.gz
+
+build:
+  binary_relocation: False
+
+about:
+  home: https://github.com/charmbracelet/glow/
+  license: MIT

conda/glow/latest

@@ -0,0 +1 @@
+1.4.1

conda/gtags/6.6.7/build.sh

@@ -0,0 +1,5 @@
+
+
+./configure --prefix=${PREFIX}
+make
+make install

conda/gtags/6.6.7/meta.yaml

@@ -0,0 +1,11 @@
+{% set version = "6.6.7" %}
+
+package:
+  name: gnu-global
+  version: {{ version }}
+
+source:
+  url: https://ftp.gnu.org/pub/gnu/global/global-{{ version }}.tar.gz
+
+about:
+  home: https://www.gnu.org/

conda/gtags/6.6.8/build.sh

@@ -0,0 +1,5 @@
+
+
+./configure --prefix=${PREFIX}
+make
+make install

conda/gtags/6.6.8/meta.yaml

@@ -0,0 +1,20 @@
+{% set version = "6.6.8" %}
+
+package:
+  name: gnu-global
+  version: {{ version }}
+
+source:
+  url: https://ftp.gnu.org/pub/gnu/global/global-{{ version }}.tar.gz
+
+requirements:
+  build:
+    - python >=3.6
+    - libiconv
+    - ncurses
+  run:
+    - libiconv
+    - ncurses
+
+about:
+  home: https://www.gnu.org/

conda/gtags/latest

@@ -0,0 +1 @@
+6.6.8

conda/neovim/0.7.0/build.sh

@@ -0,0 +1,2 @@
+
+cp -r bin lib share ${PREFIX}/

conda/neovim/0.7.0/meta.yaml

@@ -0,0 +1,12 @@
+{% set version = "0.7.0" %}
+
+package:
+  name: neovim
+  version: {{ version }}
+
+source:
+  url: https://github.com/neovim/neovim/releases/download/v{{ version }}/nvim-linux64.tar.gz
+
+about:
+  home: https://github.com/neovim/neovim/
+  license: CharityWare

conda/neovim/latest

@@ -0,0 +1 @@
+0.7.0

conda/python-neovim/0.3.1/meta.yaml

@@ -0,0 +1,37 @@
+{% set name = "python-neovim" %}
+{% set orig_name = "neovim" %}
+{% set version = "0.3.1" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  url: "https://pypi.io/packages/source/{{ orig_name[0] }}/{{ orig_name }}/{{ orig_name }}-{{ version }}.tar.gz"
+  sha256: a6a0e7a5b4433bf4e6ddcbc5c5ff44170be7d84259d002b8e8d8fb4ee78af60f
+
+build:
+  number: 0
+  script: "{{ PYTHON }} -m pip install . -vv"
+
+requirements:
+  host:
+    - pip
+    - pynvim >=0.3.1
+    - python
+  run:
+    - pynvim >=0.3.1
+    - python
+
+about:
+  home: "http://github.com/neovim/python-client"
+  license: Apache
+  license_family: APACHE
+  license_file: 
+  summary: "Transition packgage for pynvim"
+  doc_url: 
+  dev_url: 
+
+extra:
+  recipe-maintainers:
+    - your-github-id-here

conda/python-neovim/0.4.3/meta.yaml

@@ -0,0 +1,37 @@
+{% set name = "python-neovim" %}
+{% set orig_name = "neovim" %}
+{% set version = "0.4.3" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  url: "https://pypi.io/packages/source/{{ orig_name[0] }}/{{ orig_name }}/{{ orig_name }}-{{ version }}.tar.gz"
+  sha256: a6a0e7a5b4433bf4e6ddcbc5c5ff44170be7d84259d002b8e8d8fb4ee78af60f
+
+build:
+  number: 0
+  script: "{{ PYTHON }} -m pip install . -vv"
+
+requirements:
+  host:
+    - pip
+    - pynvim >=0.4.3
+    - python
+  run:
+    - pynvim >=0.4.3
+    - python
+
+about:
+  home: "http://github.com/neovim/python-client"
+  license: Apache
+  license_family: APACHE
+  license_file: 
+  summary: "Transition packgage for pynvim"
+  doc_url: 
+  dev_url: 
+
+extra:
+  recipe-maintainers:
+    - your-github-id-here

conda/python-neovim/latest

@@ -0,0 +1 @@
+0.4.3

conda/q/2.0.19/build.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+# symlink is not allowed to install
+rm -f bin/qtextasdata.py
+# six==1.11.0 version requirement is too hard
+if [[ "$($PYTHON -V | cut -d' ' -f2)" =~ "^3.8" ]]; then
+    perl -ple 's/six==([\d\.]+)/six==1.14.0/' -i.orig setup.py
+elif [[ "$($PYTHON -V | cut -d' ' -f2)" =~ "^3.9" ]]; then
+    perl -ple 's/six==([\d\.]+)/six==1.15.0/' -i.orig setup.py
+fi
+
+# install as usual
+$PYTHON setup.py install --single-version-externally-managed --record record.txt
+
+

conda/q/2.0.19/conda_build_config.yaml

@@ -0,0 +1,3 @@
+python:
+  - 3.8
+  - 3.9

conda/q/2.0.19/meta.yaml

@@ -0,0 +1,21 @@
+{% set version = "2.0.19" %}
+
+package:
+  name: q
+  version: {{ version }}
+
+source:
+  url: https://github.com/harelba/q/archive/{{ version }}.tar.gz
+
+requirements:
+  build:
+    - python {{ python }}
+    - setuptools
+    - six
+
+  run:
+    - python
+    - six
+
+about:
+  home: http://harelba.github.io/q/

conda/q/3.1.6/build.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+# symlink is not allowed to install
+rm -f bin/qtextasdata.py
+# six==1.11.0 version requirement is too hard
+if [[ "$($PYTHON -V | cut -d' ' -f2)" =~ "^3.8" ]]; then
+    perl -ple 's/six==([\d\.]+)/six==1.14.0/' -i.orig setup.py
+elif [[ "$($PYTHON -V | cut -d' ' -f2)" =~ "^3.9" ]]; then
+    perl -ple 's/six==([\d\.]+)/six==1.15.0/' -i.orig setup.py
+fi
+
+# install as usual
+$PYTHON setup.py install --single-version-externally-managed --record record.txt
+
+

conda/q/3.1.6/conda_build_config.yaml

@@ -0,0 +1,4 @@
+python:
+  - 3.8
+  - 3.9
+  - 3.10

conda/q/3.1.6/meta.yaml

@@ -0,0 +1,21 @@
+{% set version = "3.1.6" %}
+
+package:
+  name: q
+  version: {{ version }}
+
+source:
+  url: https://github.com/harelba/q/archive/refs/tags/v{{ version }}.tar.gz
+
+requirements:
+  build:
+    - python {{ python }}
+    - setuptools
+    - six
+
+  run:
+    - python
+    - six
+
+about:
+  home: http://harelba.github.io/q/

conda/q/latest

@@ -0,0 +1 @@
+3.1.6

conda/tig/2.5.4/build.sh

@@ -0,0 +1,6 @@
+
+./autogen.sh
+./configure --prefix=$PREFIX
+make
+make install
+

conda/tig/2.5.4/meta.yaml

@@ -0,0 +1,9 @@
+{% set version = "2.5.4" %}
+
+package:
+  name: tig
+  version: {{ version }}
+
+source:
+  url: https://github.com/jonas/tig/releases/download/tig-{{ version }}/tig-{{ version }}.tar.gz
+  sha256: c48284d30287a6365f8a4750eb0b122e78689a1aef8ce1d2961b6843ac246aa7

conda/tig/2.5.5/build.sh

@@ -0,0 +1,6 @@
+
+./autogen.sh
+./configure --prefix=$PREFIX
+make
+make install
+

conda/tig/2.5.5/meta.yaml

@@ -0,0 +1,8 @@
+{% set version = "2.5.5" %}
+
+package:
+  name: tig
+  version: {{ version }}
+
+source:
+  url: https://github.com/jonas/tig/releases/download/tig-{{ version }}/tig-{{ version }}.tar.gz

conda/tig/latest

@@ -0,0 +1 @@
+2.5.5

conda/tmux/3.2a/build.sh

@@ -0,0 +1,5 @@
+
+./configure --prefix=$PREFIX
+make
+make install
+

conda/tmux/3.2a/meta.yaml

@@ -0,0 +1,16 @@
+{% set version = "3.2a" %}
+
+package:
+  name: tmux
+  version: {{ version }}
+
+source:
+  url: https://github.com/tmux/tmux/releases/download/{{ version }}/tmux-{{ version }}.tar.gz
+
+requirements:
+  build:
+    - ncurses
+    - libevent
+  run:
+    - ncurses
+    - libevent

conda/tmux/latest

@@ -0,0 +1 @@
+3.2a

conda/twf/20211204/build.sh

@@ -0,0 +1,6 @@
+
+export GOPATH=$PWD
+go install github.com/wvanlint/twf/cmd/twf\@latest
+mkdir -p ${PREFIX}/bin
+cp ${GOPATH}/bin/twf ${PREFIX}/bin/twf
+

conda/twf/20211204/meta.yaml

@@ -0,0 +1,12 @@
+{% set version = "20211204" %}
+
+package:
+  name: twf
+  version: {{ version }}
+
+requirements:
+  build:
+    - go >=1.17
+
+about:
+  home: https://github.com/wvanlint/twf/

conda/twf/latest

@@ -0,0 +1 @@
+20211204