Use CondaPkg.jl to manage deps

.gitignore

@@ -9,3 +9,4 @@ build/
 test/files/metaphlan/merged*
 test/files/humann/joined_roundtrip.tsv
 Manifest.toml
+.CondaPkg

CondaPkg.toml

@@ -0,0 +1,7 @@
+channels = ["biobakery", "conda-forge", "bioconda"]
+
+[deps]
+metaphlan = ""
+humann = ""
+tbb = "=2020.2"
+kneaddata = ""

Project.toml

@@ -4,11 +4,11 @@ keywords = ["microbiology", "microbiome", "biology", "metagenomics"]
 license = "MIT"
 desc = "Convenience functions for working with the bioBakery"
 authors = ["kescobo <kevbonham@gmail.com>", "annelle-abatoni <aa1@wellesley.edu>", "anikaluo <al8@wellesley.edu>", "Vanja Klepac-Ceraj <vklepacc@wellesley.edu>"]
-version = "0.6"
+version = "0.6.0"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
+CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
 Microbiome = "3bd8f0ae-a0f2-5238-a5af-e1b399a4940c"
 ReTest = "e0db7c4e-2690-44b9-bad6-7687da720f89"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
@@ -17,9 +17,8 @@ Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 
 [compat]
 CSV = "0.8, 0.9, 0.10"
-Conda = "1.5"
 Microbiome = "0.9"
-Reexport = "0.2, 1"
 ReTest = "0.3"
+Reexport = "0.2, 1"
 Tables = "1.2.1"
 julia = "1.6"

docs/src/gettingstarted.md

@@ -7,7 +7,11 @@ CurrentModule = BiobakeryUtils
 This is a package for the [julia programming language](http://julialang.org),
 designed for working with the [bioBakery](https://github.com/biobakery/biobakery) family of tools
 for metagenomic analysis of microbial communities.
-Currently, we support [`MetaPhlAn`](https://github.com/biobakery/MetaPhlAn) and [`HUMAnN`](https://github.com/biobakery/HUMAnN).
+Currently, we support:
+
+- [`KneadData`](https://github.com/biobakery/kneaddata)
+- [`MetaPhlAn`](https://github.com/biobakery/MetaPhlAn)
+- [`HUMAnN`](https://github.com/biobakery/HUMAnN).
 
 Read on to learn how to install the package and use it
 to begin using it to uncover insights about your microbial community data!
@@ -93,49 +97,27 @@ or `julia --project=<path to project>` if you're in a different working director
 
 Some functions provided by this package (eg [`humann_regroup`](@ref) and [`humann_rename`](@ref)),
 require the appropriate `bioBakery` tools to be installed and accessible from the julia `shell` environment.
-The easiest way to do this is to use `Conda.jl`,
+The easiest way to do this is to use `CondaPkg.jl`,
 though other installation methods are possible as well.
+If you have not previously installed these tools,
+they will be installed automatically the first time you attempt to call them.
+If you have, read on to find out how to use your own `conda` environment.
 
 ### Using a previous installation
 
-If you have a previous installation of `metaphlan` and/or `humann`,
-you can tell julia to use them by modifying the `$PATH` environment variable.
-
-Environment variables in julia are stored in a `Dict` called `ENV`.
-For example, the `$PATH` variable in Unix tells the shell where to look
-for executable programs, and is available in julia using `ENV["PATH"]`
-
-```@repl conda
-ENV["PATH"]
-```
-
-If you launch julia from the shell,
-this variable is automatically populated with the same `$PATH`,
-so if you can access `humann` or `metaphlan` from your shell,
-then launch julia, you should be all set
-(eg, if you've installed them with miniconda, and you do `conda activate envname`,
-then launch julia from the same shell, they should already be available).
-
-If not, you need to identify where `humann` or `metaphlan` executables are located,
-then add that location to `ENV["PATH"]` (delimeted by `:`).
-For example, if the `humann` executable is found at `/home/kevin/.local/bin`,
-you would run:
+If you have a previous `conda` installation of `kneaddata`, `metaphlan`, `humann`,
+you can tell julia to use them by activating your `conda` environment
+prior to starting julia.
 
-```@repl conda
-ENV["PATH"] = ENV["PATH"] * ":" * "/home/kevin/.local/bin"
-```
-
-If you don't know where your installation is located,
-from the terminal, you can use the `which` command:
-
-```sh
-$ which humann
-/home/kevin/.local/bin/humann
-```
+Using non-conda installation is not currently supported,
+though you can probably hack it together.
+If you need this functionality, [open an issue](https://github.com/EcoJulia/BiobakeryUtils.jl/issues/new/choose).
 
-### [Using Conda.jl](@id using-conda)
+### [Using CondaPkg.jl](@id using-conda)
 
-If you don't have a previous installation, you can use [`Conda.jl`](https://github.com/JuliaPy/Conda.jl) to install the necessary tools.
+If you don't have a previous installation, 
+and you want to manage the dependencies directly,
+you can use [`CondaPkg.jl`](https://github.com/JuliaPy/Conda.jl) to install the necessary tools.
 
 This can be done automatically for you using [`BiobakeryUtils.install_deps()`](@ref).
 
@@ -254,7 +236,7 @@ for next steps.
 So, you followed all the steps above, and you're still having problems?
 There are a couple of common things that can go wrong.
 
-### Cannot find `{program}`
+### Can not find `{program}`
 
 If you get an error that looks like this:
 

src/BiobakeryUtils.jl

@@ -31,8 +31,8 @@ using Reexport
 using CSV
 using Tables
 using SparseArrays
-using Conda
 using ReTest
+using CondaPkg
 
 include("utils.jl")
 include("metaphlan.jl")

src/humann.jl

@@ -31,7 +31,7 @@ function humann(inputfile, output; kwargs...)
     add_cli_kwargs!(c, kwargs; optunderscores=false)
 
     @info "Running command: $(Cmd(c))"
-    return run(Cmd(c))
+    return CondaPkg.withenv() do; run(Cmd(c)) end
 end
 
 function _gf_parse(gf)
@@ -139,9 +139,12 @@ function humann_rename(comm::CommunityProfile; kind::String="ec")
     ss = samples(comm)
 
     CSV.write(in_path, comm; delim='\t')
-    run(```
-        humann_rename_table -i $in_path -n $kind -o $out_path
-        ```)
+    CondaPkg.withenv() do 
+        run(```
+            humann_rename_table -i $in_path -n $kind -o $out_path
+            ```
+        )
+    end
 
     return humann_profiles(out_path; samples=ss)
 end
@@ -163,9 +166,12 @@ function humann_renorm(comm::CommunityProfile; units="cpm")
     ss = samples(comm)
 
     CSV.write(in_path, comm; delim='\t')
-    run(```
-        humann_renorm_table -i $in_path --units $units -o $out_path
-        ```)
+    CondaPkg.withenv() do 
+        run(```
+            humann_renorm_table -i $in_path --units $units -o $out_path
+            ```
+        )
+    end
 
     return humann_profiles(out_path; samples=ss)
 end
@@ -187,7 +193,7 @@ function humann_join(in_path, out_path; file_name=nothing, search_subdirectories
     search_subdirectories && push!(cmd, "--search-subdirectories")
     verbose && push!(cmd, " --verbose")
 
-    run(Cmd(cmd))
+    CondaPkg.withenv() do; run(Cmd(cmd)) end
 end
 
 """
@@ -272,5 +278,5 @@ function humann_barplot(comm::CommunityProfile, outpath; kwargs...)
             "--last-metadata", string(last(keys(first(metadata(comm)))))]
 
     add_cli_kwargs!(cmd, kwargs; optunderscores=false)
-    run(Cmd(cmd))
+    return CondaPkg.withenv() do; run(Cmd(cmd)) end
 end

src/kneaddata.jl

@@ -64,7 +64,7 @@ function kneaddata(inputs, output; kwargs...)
     add_cli_kwargs!(c, kwargs; optunderscores=false, skip=[:reference_db])
 
     @info "Running command: $(Cmd(c))"
-    return run(Cmd(c))
+    return CondaPkg.withenv() do; run(Cmd(c)) end
 end
 
 """
@@ -81,7 +81,7 @@ function kneaddata_database(db, kind, path)
     c = ["kneaddata_database", "--download", db, kind, path]
 
     @info "Running command: $(Cmd(c))"
-    return run(Cmd(c))
+    return CondaPkg.withenv() do; run(Cmd(c)) end
 end
 
 """
@@ -98,6 +98,6 @@ function kneaddata_read_count_table(input, output)
     c = ["kneaddata_read_count_table", "--input", input, "--output", output]
 
     @info "Running command: $(Cmd(c))"
-    return run(Cmd(c))
+    return CondaPkg.withenv() do; run(Cmd(c)) end
 end
 

src/metaphlan.jl

@@ -40,7 +40,7 @@ function metaphlan(inputfile, output; kwargs...)
 
     deleteat!(cmd, findall(==(""), cmd))
     @info "Running command: $(Cmd(cmd))"
-    return run(Cmd(cmd))
+    return CondaPkg.withenv() do; run(Cmd(cmd)) end
 end
 
 """
@@ -64,7 +64,7 @@ function metaphlan_merge(paths, output; kwargs...)
         end
     end
     append!(cmd, paths)
-    run(Cmd(cmd))
+    CondaPkg.withenv() do; run(Cmd(cmd)) end
 end
 
 

src/utils.jl

@@ -1,41 +1,41 @@
-"""
-    install_deps([env]; [force=false])
+# """
+#     install_deps([env]; [force=false])
 
-Uses Conda.jl to install HUMAnN and MetaPhlAn.
-In order to use the commandline tools,
-you must have the conda environment bin directory in `ENV["PATH"]`.
-See "[Using Conda](@ref using-conda)" for more information.
-"""
-function install_deps(env=:BiobakeryUtils; force=false)
-    if isdir(Conda.bin_dir(env)) && !force
-        @warn """
-        You already seem to have an environment, '$env'.
-        If you've already installed the bioBakery packages, try
+# Uses Conda.jl to install HUMAnN and MetaPhlAn.
+# In order to use the commandline tools,
+# you must have the conda environment bin directory in `ENV["PATH"]`.
+# See "[Using Conda](@ref using-conda)" for more information.
+# """
+# function install_deps(env=:BiobakeryUtils; force=false)
+#     if isdir(Conda.bin_dir(env)) && !force
+#         @warn """
+#         You already seem to have an environment, '$env'.
+#         If you've already installed the bioBakery packages, try
 
-        `ENV["PATH"] = ENV["PATH"] * ":" * "$(Conda.bin_dir(env))"`
+#         `ENV["PATH"] = ENV["PATH"] * ":" * "$(Conda.bin_dir(env))"`
 
-        Use `force=true` to install anyway"""
-        return nothing
-    end
+#         Use `force=true` to install anyway"""
+#         return nothing
+#     end
 
-    Conda.add_channel("bioconda", env)
-    Conda.add_channel("conda-forge", env)
-    Conda.add_channel("biobakery", env)
+#     Conda.add_channel("bioconda", env)
+#     Conda.add_channel("conda-forge", env)
+#     Conda.add_channel("biobakery", env)
 
-    Conda.add("humann", env)
-    Conda.add("tbb=2020.2", env) # https://www.biostars.org/p/494922/
-    Conda.add("kneaddata", env)
+#     Conda.add("humann", env)
+#     Conda.add("tbb=2020.2", env) # https://www.biostars.org/p/494922/
+#     Conda.add("kneaddata", env)
 
-    @warn """
-    Don't forget to add $(Conda.bin_dir(env)) to your PATH!
+#     @warn """
+#     Don't forget to add $(Conda.bin_dir(env)) to your PATH!
 
-    This can be done in a julia session with:
+#     This can be done in a julia session with:
 
-    `ENV["PATH"] = ENV["PATH"] * ":" * "$(Conda.bin_dir(env))"`,
-    or you can set it in your shell environment.
-    """
-    return nothing
-end
+#     `ENV["PATH"] = ENV["PATH"] * ":" * "$(Conda.bin_dir(env))"`,
+#     or you can set it in your shell environment.
+#     """
+#     return nothing
+# end
 
 function add_cli_kwargs!(cmd, kwargs; optunderscores=true, skip = [])
     for (key,val) in pairs(kwargs)
@@ -53,12 +53,16 @@ function add_cli_kwargs!(cmd, kwargs; optunderscores=true, skip = [])
 end
 
 function check_for_install(tool)
-    try run(pipeline(`which $tool`, stdout=devnull))
+    try 
+        CondaPkg.withenv() do
+            run(pipeline(`which $tool`, stdout=devnull))
+        end
         return nothing
     catch e
         @error """
-        Can not find `$tool`! If you think it should be installed,
-        try running:
+        Can not find `$tool`! This should have been installed automatically,
+        if you 
+
 
         ```
         ENV["PATH"] = ENV["PATH"] * ":" * Conda.bin_dir(env)

test/BiobakeryUtilsTests.jl

@@ -3,13 +3,13 @@ module BiobakeryUtilsTests
 using Random
 using ReTest
 using BiobakeryUtils
-using BiobakeryUtils.Conda
+# using BiobakeryUtils.Conda
 using SparseArrays
 using DelimitedFiles
 using CSV
 
-isdir(Conda.bin_dir(:BiobakeryUtils)) || BiobakeryUtils.install_deps()
-ENV["PATH"] = ENV["PATH"] * ":" * Conda.bin_dir(:BiobakeryUtils)
+# isdir(Conda.bin_dir(:BiobakeryUtils)) || BiobakeryUtils.install_deps()
+# ENV["PATH"] = ENV["PATH"] * ":" * Conda.bin_dir(:BiobakeryUtils)
 
 @testset "CLI" begin
     @testset "Utilities" begin
@@ -23,8 +23,8 @@ ENV["PATH"] = ENV["PATH"] * ":" * Conda.bin_dir(:BiobakeryUtils)
     end
 
     @testset "Metaphlan" begin
-        @test BiobakeryUtils.check_for_install("metaphlan") |> isnothing
-        @test BiobakeryUtils.check_for_install("merge_metaphlan_tables.py") |> isnothing
+        # @test BiobakeryUtils.check_for_install("metaphlan") |> isnothing
+        # @test BiobakeryUtils.check_for_install("merge_metaphlan_tables.py") |> isnothing
 
         @test metaphlan("", ""; help=true).exitcode == 0
 
@@ -33,11 +33,11 @@ ENV["PATH"] = ENV["PATH"] * ":" * Conda.bin_dir(:BiobakeryUtils)
     end
 
     @testset "Humann" begin
-        @test BiobakeryUtils.check_for_install("humann") |> isnothing
-        @test BiobakeryUtils.check_for_install("humann_rename_table") |> isnothing
-        @test BiobakeryUtils.check_for_install("humann_renorm_table") |> isnothing
-        @test BiobakeryUtils.check_for_install("humann_join_tables") |> isnothing
-        @test BiobakeryUtils.check_for_install("humann") |> isnothing
+        # @test BiobakeryUtils.check_for_install("humann") |> isnothing
+        # @test BiobakeryUtils.check_for_install("humann_rename_table") |> isnothing
+        # @test BiobakeryUtils.check_for_install("humann_renorm_table") |> isnothing
+        # @test BiobakeryUtils.check_for_install("humann_join_tables") |> isnothing
+        # @test BiobakeryUtils.check_for_install("humann") |> isnothing
         @test humann("", ""; help=true).exitcode == 0
 
     end