Source Mage code commit list

[Ismael Luceno <scm AT sourcemage.org>]

GIT changes to master grimoire by Ismael Luceno <ismael AT sourcemage.org>:

 ChangeLog                    |    3 ++
 science-libs/biolibc/BUILD   |    4 +++
 science-libs/biolibc/DETAILS |   46 
+++++++++++++++++++++++++++++++++++++++++++
 science-libs/biolibc/HISTORY |    2 +
 science-libs/biolibc/INSTALL |    2 +
 5 files changed, 57 insertions(+)

New commits:
commit 28976b68457a453f07ffc6d95dececfbd74aaf42
Author: Ismael Luceno <ismael AT sourcemage.org>
Commit: Ismael Luceno <ismael AT sourcemage.org>

    biolibc: new spell, High-performance, memory-efficient bioinformatics 
library

diff --git a/ChangeLog b/ChangeLog
index 887a744..37fe1f1 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,6 @@
+2022-10-23 Ismael Luceno <ismael AT sourcemage.org>
+       * science-libs/biolibc: new spell, High-performance, memory-efficient 
bioinformatics library
+
 2022-10-19 Treeve Jelbert <treeve AT sourcemage.org>
        * qt6/FUNCTIONS: fix build for some AMD cpus
          fixes at le t6{base, declarative.svg}
diff --git a/science-libs/biolibc/BUILD b/science-libs/biolibc/BUILD
new file mode 100755
index 0000000..6574cf3
--- /dev/null
+++ b/science-libs/biolibc/BUILD
@@ -0,0 +1,4 @@
+${MAKE:-make} -j "$MAKE_NJOBS" \
+             CC="${CC:-cc}" \
+             HOSTCC="${HOSTCC:-${CC:-cc}}" \
+             PREFIX="$INSTALL_ROOT"/usr
diff --git a/science-libs/biolibc/DETAILS b/science-libs/biolibc/DETAILS
new file mode 100755
index 0000000..f039def
--- /dev/null
+++ b/science-libs/biolibc/DETAILS
@@ -0,0 +1,46 @@
+           SPELL=biolibc
+         VERSION=0.2.3
+          SOURCE="$SPELL-$VERSION.tar.gz"
+   
SOURCE_URL[0]=https://github.com/auerlab/$SPELL/archive/refs/tags/$VERSION.tar.gz
+     
SOURCE_HASH=sha512:53fa93189517d3632b5cacadeae1d61eef725b5381be15cadb4150e08dbd2bce9e5788cdc71f40bbd658b3c64ba7521436f7cad6676ce92dac735e769f92f24d
+SOURCE_DIRECTORY="$BUILD_DIRECTORY/$SPELL-$VERSION"
+        WEB_SITE="https://github.com/auerlab/biolibc";
+      LICENSE[0]="BSD-2-Clause"
+         ENTERED=20221023
+        KEYWORDS=""
+           SHORT="High-performance, memory-efficient bioinformatics library"
+cat << EOF
+Many bioinformatics pipelines are essentially made of mud and straw;
+quick-and-dirty single-use scripts written in various interpreted languages,
+with little or no meaningful error reporting or documentation, and generally
+poor performance.
+
+Biolibc is a collection of high-quality bricks that can be used to build
+efficient, robust software applications to replace disposable scripts. Using
+biolibc, you can easily develop permanent solutions that are easy to use and
+install, with near-optimal performance, so that no one ever need reinvent
+that particular wheel. Biolibc also facilitates development of more complex
+applications by providing many commonly used building blocks, thus releasing
+you from low-level coding.
+
+For some examples, see biolibc-tools, vcf-split, ad2vcf, vcf2hap,
+haploh-vcf-depths, peak-classifier, generand, ad-matrix, and fastq-trim.
+
+In more technical terms, biolibc is a library of fast, memory-efficient C
+functions for processing biological data. Like libc, it consists of numerous
+disparate, general-purpose functions that can be used by a wide variety
+of applications.
+
+These include functions for reading and writing common file formats such
+as BED, GFF, FASTA, FASTQ, SAM and VCF, string functions specific to
+bioinformatics such as chromosome_name_cmp(), detecting feature overlaps, 
etc.
+
+Biolibc, and the more generic libxtend, move your C coding to a higher
+level by providing the most basic building blocks and additional software
+layers commonly needed in bioinformatics programming. Using C and biolibc,
+you can write simple, near-optimal C programs that may be orders of magnitude
+faster than scripting languages such as Perl, Python, and R, while requiring
+comparable coding effort. fastx-derep.c, a 1-page C program for dereplicating
+FASTA/FASTQ files, offers a great example of how the right libraries 
eliminate
+the need for low-level programming in C.
+EOF
diff --git a/science-libs/biolibc/HISTORY b/science-libs/biolibc/HISTORY
new file mode 100644
index 0000000..85e72b7
--- /dev/null
+++ b/science-libs/biolibc/HISTORY
@@ -0,0 +1,2 @@
+2022-10-23 Ismael Luceno <ismael AT sourcemage.org>
+       * BUILD, DETAILS, INSTALL: spell created
diff --git a/science-libs/biolibc/INSTALL b/science-libs/biolibc/INSTALL
new file mode 100755
index 0000000..87c6a5e
--- /dev/null
+++ b/science-libs/biolibc/INSTALL
@@ -0,0 +1,2 @@
+${MAKE:-make} install \
+             PREFIX="$INSTALL_ROOT"/usr