From f26b69cdae9cb54087cd990e7cd84a46a8b8d65f Mon Sep 17 00:00:00 2001
From: ivuorinen <ivuorinen@users.noreply.github.com>
Date: Wed, 15 May 2024 00:14:04 +0000
Subject: [PATCH] Update cheatsheets

---
 tldr/gleam     | 41 +++++++++++++++++++++++++++++++++++++++++
 tldr/linux/bwa | 30 ++++++++++++++++++++++++++++++
 tldr/lstopo    | 29 +++++++++++++++++++++++++++++
 3 files changed, 100 insertions(+)
 create mode 100644 tldr/gleam
 create mode 100644 tldr/linux/bwa
 create mode 100644 tldr/lstopo

diff --git a/tldr/gleam b/tldr/gleam
new file mode 100644
index 00000000..7f5698b5
--- /dev/null
+++ b/tldr/gleam
@@ -0,0 +1,41 @@
+---
+syntax: markdown
+tags: [tldr, common]
+source: https://github.com/tldr-pages/tldr.git
+---
+# gleam
+
+> The compiler, build tool, package manager and code formatter for Gleam, "a friendly language for building type-safe systems that scale!".
+> More information: <https://gleam.run/writing-gleam/command-line-reference/>.
+
+- Create a new gleam project:
+
+`gleam new {{project_name}}`
+
+- Build and run a gleam project:
+
+`gleam run`
+
+- Build the project:
+
+`gleam build`
+
+- Run a project for a particular platform and runtime:
+
+`gleam run --target {{platform}} --runtime {{runtime}}`
+
+- Add a hex dependency to your project:
+
+`gleam add {{dependency_name}}`
+
+- Run project tests:
+
+`gleam test`
+
+- Format source code:
+
+`gleam format`
+
+- Type check the project:
+
+`gleam check`
diff --git a/tldr/linux/bwa b/tldr/linux/bwa
new file mode 100644
index 00000000..5ff37f74
--- /dev/null
+++ b/tldr/linux/bwa
@@ -0,0 +1,30 @@
+---
+syntax: markdown
+tags: [tldr, linux]
+source: https://github.com/tldr-pages/tldr.git
+---
+# bwa
+
+> Burrows-Wheeler Alignment tool.
+> Short, low-divergent DNA sequences mapper against a large reference genome, such as the human genome.
+> More information: <https://github.com/lh3/bwa>.
+
+- Index the reference genome:
+
+`bwa index {{path/to/reference.fa}}`
+
+- Map single-end reads (sequences) to indexed genome using 32 [t]hreads and compress the result to save space:
+
+`bwa mem -t 32 {{path/to/reference.fa}} {{path/to/read_single_end.fq.gz}} | gzip > {{path/to/alignment_single_end.sam.gz}}`
+
+- Map pair-end reads (sequences) to the indexed genome using 32 [t]hreads and compress the result to save space:
+
+`bwa mem -t 32 {{path/to/reference.fa}} {{path/to/read_pair_end_1.fq.gz}} {{path/to/read_pair_end_2.fq.gz}} | gzip > {{path/to/alignment_pair_end.sam.gz}}`
+
+- Map pair-end reads (sequences) to the indexed genome using 32 [t]hreads with [M]arking shorter split hits as secondary for output SAM file compatibility in Picard software and compress the result:
+
+`bwa mem -M -t 32 {{path/to/reference.fa}} {{path/to/read_pair_end_1.fq.gz}} {{path/to/read_pair_end_2.fq.gz}} | gzip > {{path/to/alignment_pair_end.sam.gz}}`
+
+- Map pair-end reads (sequences) to indexed genome using 32 [t]hreads with FASTA/Q [C]omments (e.g. BC:Z:CGTAC) appending to a compressed result:
+
+`bwa mem -C -t 32 {{path/to/reference.fa}} {{path/to/read_pair_end_1.fq.gz}} {{path/to/read_pair_end_2.fq.gz}} | gzip > {{path/to/alignment_pair_end.sam.gz}}`
diff --git a/tldr/lstopo b/tldr/lstopo
new file mode 100644
index 00000000..e1f6e604
--- /dev/null
+++ b/tldr/lstopo
@@ -0,0 +1,29 @@
+---
+syntax: markdown
+tags: [tldr, common]
+source: https://github.com/tldr-pages/tldr.git
+---
+# lstopo
+
+> Show the hardware topology of the system.
+> More information: <https://manned.org/lstopo>.
+
+- Show the summarized system topology in a graphical window (or print to console if no graphical display is available):
+
+`lstopo`
+
+- Show the full system topology without summarizations:
+
+`lstopo --no-factorize`
+
+- Show the summarized system topology with only [p]hysical indices (i.e. as seen by the OS):
+
+`lstopo --physical`
+
+- Write the full system topology to a file in the specified format:
+
+`lstopo --no-factorize --output-format {{console|ascii|tex|fig|svg|pdf|ps|png|xml}} {{path/to/file}}`
+
+- Output in monochrome or greyscale:
+
+`lstopo --palette {{none|grey}}`