lsaBGC/lsaBGC_env.yml at main · Kalan-Lab/lsaBGC · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
name: lsaBGC
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - python>=3.9
  - setuptools<=58.2.0
  - pip=22.1.2
  - conda-forge::cxx-compiler
  - conda-forge::biopython=1.79
  - bioconda::pysam=0.16.0.1
  - bioconda::bowtie2=2.4.5
  - bioconda::samtools=1.12
  - bioconda::mafft=7.505
  - bioconda::mcl=14.137
  - bioconda::pal2nal=14.1
  - bioconda::hmmer=3.3.2
  - bioconda::orthofinder=2.5.4
  - bioconda::panaroo
  - bioconda::fasttree=2.1.11
  - conda-forge::ete3=3.1.2
  - bioconda::diamond=2.0.15
  - conda-forge::r-base
  - conda-forge::r-ggplot2
  - conda-forge::r-cowplot
  - conda-forge::r-phytools
  - conda-forge::r-ape
  - conda-forge::r-scatterpie
  - conda-forge::r-dplyr
  - conda-forge::r-gggenes
  - bioconda::bioconductor-ggtree
  - conda-forge::r-ggalluvial
  - conda-forge::r-data.table
  - conda-forge::r-plyr
  - conda-forge::r-gridextra
  - bioconda::prodigal
  - bioconda::pyrodigal=2.3.0
  - conda-forge::tar
  - conda-forge::pandas
  - conda-forge::pomegranate=0.13.3
  - bioconda::mash
  - bioconda::gtotree=1.8.10
  - conda-forge::xlsxwriter=3.0.3
  - bioconda::ncbi-genome-download
  - bioconda::gecco=0.9.6
  - bioconda::n50
  - conda-forge::networkx
  - conda-forge::scipy
  - conda-forge::scikit-learn
  - conda-forge::numpy