From f9b15972ea9070e5cba0b8f2191bd921f010461d Mon Sep 17 00:00:00 2001
From: james94 <james94@mi.fu-berlin.de>
Date: Mon, 8 Aug 2022 11:52:13 +0200
Subject: [PATCH] change names for environments

---
 envs/AUXILIARY_PYTHON_SCRIPTS.yaml | 13 +++++++++++++
 envs/AUXILIARY_R_SCRIPTS.yaml      | 11 +++++++++++
 envs/BUSCO.yaml                    | 19 +++++++++++++++++++
 envs/HiC_CONTACT_MAPS.yaml         |  9 +++++++++
 envs/MERYL_MERQURY.yaml            | 18 ++++++++++++++++++
 envs/UNZIP_and_QC.yaml             | 11 +++++++++++
 6 files changed, 81 insertions(+)
 create mode 100644 envs/AUXILIARY_PYTHON_SCRIPTS.yaml
 create mode 100644 envs/AUXILIARY_R_SCRIPTS.yaml
 create mode 100644 envs/BUSCO.yaml
 create mode 100644 envs/HiC_CONTACT_MAPS.yaml
 create mode 100644 envs/MERYL_MERQURY.yaml
 create mode 100644 envs/UNZIP_and_QC.yaml

diff --git a/envs/AUXILIARY_PYTHON_SCRIPTS.yaml b/envs/AUXILIARY_PYTHON_SCRIPTS.yaml
new file mode 100644
index 0000000..fb91762
--- /dev/null
+++ b/envs/AUXILIARY_PYTHON_SCRIPTS.yaml
@@ -0,0 +1,13 @@
+channels:
+ - conda-forge
+ - bioconda
+ - anaconda
+dependencies:
+ - tabulate=0.8.7
+ - beautifulsoup4=4.9
+ - pandoc=2.15.*
+ - tectonic
+ - wkhtmltopdf
+ - pandas
+ - numpy
+ - ghostscript
diff --git a/envs/AUXILIARY_R_SCRIPTS.yaml b/envs/AUXILIARY_R_SCRIPTS.yaml
new file mode 100644
index 0000000..1d3713d
--- /dev/null
+++ b/envs/AUXILIARY_R_SCRIPTS.yaml
@@ -0,0 +1,11 @@
+channels:
+ - bioconda
+ - conda-forge
+dependencies:
+  - python >=3.10.4
+  - r-argparse=2.1.5=r41hc72bb7e_0
+  - r-base >=4.1.3
+  - r-minpack.lm=1.2_2=r41h1463581_0
+  - genomescope2=2.0=py310r41hdfd78af_5
+  - r-dplyr==1.0.9
+  - r-formattable==0.2.1
diff --git a/envs/BUSCO.yaml b/envs/BUSCO.yaml
new file mode 100644
index 0000000..30dba8d
--- /dev/null
+++ b/envs/BUSCO.yaml
@@ -0,0 +1,19 @@
+channels:
+ - conda-forge
+ - bioconda
+ - anaconda
+ - defaults
+dependencies:
+  - augustus >=3.3
+  - biopython
+  - blast >=2.10.1
+  - fonts-conda-ecosystem
+  - hmmer >=3.1b2
+  - metaeuk
+  - pandas
+  - prodigal
+  - python >=3.3
+  - r-base
+  - r-ggplot2 >=2.2.1
+  - sepp >=4.3.10
+  - busco == 5.3.0
diff --git a/envs/HiC_CONTACT_MAPS.yaml b/envs/HiC_CONTACT_MAPS.yaml
new file mode 100644
index 0000000..571f432
--- /dev/null
+++ b/envs/HiC_CONTACT_MAPS.yaml
@@ -0,0 +1,9 @@
+channels:
+ - anaconda
+ - bioconda
+ - conda-forge
+dependencies:
+ - pretextmap == 0.1.9
+ - pretextsnapshot == 0.0.4
+ - bwa-mem2 == 2.2.1
+ - samtools == 1.14
diff --git a/envs/MERYL_MERQURY.yaml b/envs/MERYL_MERQURY.yaml
new file mode 100644
index 0000000..9d7c900
--- /dev/null
+++ b/envs/MERYL_MERQURY.yaml
@@ -0,0 +1,18 @@
+channels:
+ - bioconda
+ - defaults
+ - conda-forge
+dependencies:
+  - merqury == 1.3
+  - bedtools == 2.29.2
+  - meryl == 1.3
+  - cairo == 1.16
+  - openjdk == 11.0.13
+  - r-argparse == 2.1.5
+  - r-base >=4.0,<4.1.0a0
+  - r-ggplot2=3.3.2=r40hc72bb7e_1
+  - r-scales == 1.2.0
+  - samtools == 1.15.1
+  - xorg-libxrender == 0.9.10
+  - xorg-libxext == 1.3.4
+  - xorg-libxau == 1.0.9
diff --git a/envs/UNZIP_and_QC.yaml b/envs/UNZIP_and_QC.yaml
new file mode 100644
index 0000000..e50ba80
--- /dev/null
+++ b/envs/UNZIP_and_QC.yaml
@@ -0,0 +1,11 @@
+channels:
+ - anaconda
+ - bioconda
+ - conda-forge
+dependencies:
+ - pigz=2.4
+ - trim-galore=0.6.6
+ - pandoc=2.11
+ - multiqc=1.9
+ - python=3.8.5
+ - trimmomatic=0.39
-- 
GitLab