From 143933c0b6aa637deb1ad8e8361d83e00197a033 Mon Sep 17 00:00:00 2001
From: MillironX <25492070+MillironX@users.noreply.github.com>
Date: Tue, 10 Aug 2021 17:50:08 -0500
Subject: [PATCH] Give assembly_improvement a pretty README

---
 assembly_improvement/README.md                | 37 +++++++++++++++++++
 assembly_improvement/assembly_improvement.def |  4 +-
 2 files changed, 39 insertions(+), 2 deletions(-)
 create mode 100644 assembly_improvement/README.md

diff --git a/assembly_improvement/README.md b/assembly_improvement/README.md
new file mode 100644
index 0000000..c38b5b6
--- /dev/null
+++ b/assembly_improvement/README.md
@@ -0,0 +1,37 @@
+# Assembly Improvement
+
+[![Container source](https://img.shields.io/static/v1?label=Container%20Source&message=GitHub&color=lightgrey&logo=github&style=flat-square)](https://github.com/MillironX/singularity-builds/tree/master/assembly_improvement)
+[![assembly_improvement source](https://img.shields.io/static/v1?label=assembly_improvement%20Source&message=GitHub&color=lightgrey&logo=github&style=flat-square)](https://github.com/sanger-pathogens/assembly_improvement)
+[![Version 1.160490](https://img.shields.io/static/v1?label=Latest%20version&message=1.160490&color=yellowgreen&logo=linuxcontainers&style=flat-square)](https://cloud.sylabs.io/library/millironx/default/assembly_improvement)
+[![Docs](https://img.shields.io/static/v1?label=Docs&message=README&color=blue&style=flat-square)](https://github.com/sanger-pathogens/assembly_improvement/blob/master/README.md)
+[![CentOS base](https://img.shields.io/static/v1?label=Base%20image&message=CentOS&color=9fcf32&logo=centos&style=flat-square)](https://www.centos.org/)
+
+Take in an assembly in FASTA format, reads in FASTQ format, and make the
+assembly better by scaffolding and gap filling.
+
+## Tools installed
+
+### SSPACE
+
+- `SSPACE_Basic.pl`
+
+### GapFiller
+
+- `GapFiller`
+
+### Abacas
+
+- `abacas.pl`
+
+### SGA
+
+- `sga`
+
+### improve_assembly
+
+- `improve_assembly`
+- `diginorm_with_khmer`
+- `fill_gaps_with_gapfiller`
+- `order_contigs_with_abacas`
+- `read_correction_with_sga`
+- `scaffold_with_sspace`
diff --git a/assembly_improvement/assembly_improvement.def b/assembly_improvement/assembly_improvement.def
index 51057dc..a6458a6 100644
--- a/assembly_improvement/assembly_improvement.def
+++ b/assembly_improvement/assembly_improvement.def
@@ -11,7 +11,7 @@ From: default/centos:latest
   dnf config-manager --set-enabled PowerTools
 
   # Operating dependencies
-  dnf --setopt=install_weak_deps=False install procps perl python3 -y
+  dnf --setopt=install_weak_deps=False install procps perl python3 which -y
 
   # Building dependencies
   dnf groupinstall 'Development Tools' -y
@@ -152,7 +152,7 @@ From: default/centos:latest
 %labels
   Author 25492070+MillironX@users.noreply.github.com
   SoftwareVersion 1.160490
-  SingularityDefinitionVersion 1
+  SingularityDefinitionVersion 2
 
 %help
   Assembly Improvement