swap simuG to conda-based install

.github/workflows/tests.yml

@@ -689,25 +689,25 @@ jobs:
         shell: micromamba-shell {0}
         run: |
           harpy simulate snpindel --quiet --snp-count 10 --indel-count 10 -z 0.5  test/genome/genome.fasta.gz
-          harpy simulate snpindel --quiet --prefix Simulate/snpvcf --snp-vcf Simulate/snpindel/diploid/sim.snp.hap1.vcf --indel-vcf Simulate/snpindel/diploid/sim.indel.hap1.vcf  test/genome/genome.fasta.gz
+          harpy simulate snpindel --quiet --prefix Simulate/snpvcf --snp-vcf Simulate/snpindel/haplotype_1/sim.hap1.snp.vcf --indel-vcf Simulate/snpindel/haplotype_1/sim.hap1.indel.vcf  test/genome/genome.fasta.gz
       - name: simulate inversions
         shell: micromamba-shell {0}
         if: always()
         run: |
           harpy simulate inversion --quiet --count 10 -z 0.5 test/genome/genome.fasta.gz
-          harpy simulate inversion --quiet --prefix Simulate/invvcf --vcf Simulate/inversion/diploid/sim.inversion.hap1.vcf  test/genome/genome.fasta.gz
+          harpy simulate inversion --quiet --prefix Simulate/invvcf --vcf Simulate/inversion/haplotype_1/sim.hap1.inversion.vcf  test/genome/genome.fasta.gz
       - name: simulate cnv
         shell: micromamba-shell {0}
         if: always()
         run: |
           harpy simulate cnv --quiet --count 10 -z 0.5 test/genome/genome.fasta.gz
-          harpy simulate cnv --quiet --prefix Simulate/cnvvcf --vcf Simulate/cnv/diploid/sim.cnv.hap1.vcf  test/genome/genome.fasta.gz
+          harpy simulate cnv --quiet --prefix Simulate/cnvvcf --vcf Simulate/cnv/haplotype_1/sim.hap1.cnv.vcf  test/genome/genome.fasta.gz
       - name: simulate translocations
         shell: micromamba-shell {0}
         if: always()
         run: |
           harpy simulate translocation --quiet --count 10 -z 0.5 test/genome/genome.fasta.gz
-          harpy simulate translocation --quiet --prefix Simulate/transvcf --vcf Simulate/translocation/diploid/sim.translocation.hap1.vcf  test/genome/genome.fasta.gz
+          harpy simulate translocation --quiet --prefix Simulate/transvcf --vcf Simulate/translocation/haplotype_1/sim.hap1.translocation.vcf  test/genome/genome.fasta.gz
 
   simulate_linkedreads:
     needs: [changes, pkgbuild]

.gitignore

@@ -1,6 +1,5 @@
 .snakemake/
 .vscode/
-.harpy_envs/
 .condarc
 .cache/
 hpc/

harpy/_cli_types_generic.py

@@ -56,6 +56,7 @@ def convert(self, value, param, ctx):
 
 class InputFile(click.ParamType):
     """A class for a click type that verifies that a file exists and that it has an expected extension"""
+    name = "input_file"
     def __init__(self, filetype, gzip_ok):
         super().__init__()
         self.filetype = filetype

harpy/_conda.py

@@ -1,12 +1,17 @@
 """Creates environment recipes for all the Harpy workflows"""
 
 import os
+import sys
+import yaml
+from rich import box
+from rich.table import Table
+from rich import print as rprint
+from ._printing import print_error, print_solution_with_culprits
 
-def create_conda_recipes():
+def create_conda_recipes(outdir: str, envs: list=None) -> None:
     """Create the YAML files of the workflow conda dependencies"""
-    condachannels = ["bioconda","conda-forge"]
     environ = {
-        "align": [
+        "align" : [
             "bioconda::bwa",
             "bioconda::ema",
             "bioconda::samtools=1.20",
@@ -17,7 +22,7 @@ def create_conda_recipes():
             "conda-forge::libzlib",
             "conda-forge::xz"
         ],
-        "assembly":[
+        "assembly" : [
             "bioconda::arcs",
             "bioconda::bwa",
             "bioconda::cloudspades",
@@ -63,36 +68,71 @@ def create_conda_recipes():
             "bioconda::perl-math-random",
             "bioconda::perl-inline-c",
             "bioconda::perl-parse-recdescent",
+            "bioconda::simug>1.0.0",
             "conda-forge::numpy",
             "conda-forge::perl"
         ],
-        "spades": [
+        "spades" : [
             "conda-forge::python=3"
         ],
         "stitch" : [
             "bioconda::r-stitch=1.6.10"
         ],
-        "variants": [
+        "variants" : [
             "bioconda::bcftools=1.20",
             "bioconda::freebayes=1.3.6",
             "bioconda::leviathan",
             "bioconda::naibr-plus"
         ]
     }
 
-    os.makedirs(".harpy_envs", exist_ok = True)
-    # overwrites existing
-    for env,deps in environ.items():
-        with open(f".harpy_envs/{env}.yaml", mode="w", encoding="utf-8") as yml:
-            yml.write(f"name: {env}\n")
-            yml.write("channels:\n  - ")
-            yml.write("\n  - ".join(condachannels))
-            yml.write("\ndependencies:\n  - ")
-            yml.write("\n  - ".join(deps) + "\n")
+    os.makedirs(f"{outdir}/workflow/envs", exist_ok = True)
+    # if none provided, use all
+    if not envs:
+        envs = environ.keys()
 
-    # post-deployment scripts
-    with open(".harpy_envs/spades.post-deploy.sh", "w", encoding="utf-8") as shellscript:
-        shellscript.write("wget -O .spades.tar.gz https://github.com/ablab/spades/releases/download/v4.0.0/SPAdes-4.0.0-Linux.tar.gz\n")
-        shellscript.write("tar -xvzf .spades.tar.gz && rm .spades.tar.gz\n")
-        shellscript.write("mv SPAdes-4.0.0-Linux/bin/* ${CONDA_PREFIX}/bin && mv SPAdes-4.0.0-Linux/share/* ${CONDA_PREFIX}/share\n")
-        shellscript.write("rm -r SPAdes-4.0.0-Linux\n")
+    for i in envs:
+        try:
+            env_dict = {
+                "name" : i,
+                "channels" : ["bioconda","conda-forge"],
+                "dependencies": environ[i]
+            }
+        except KeyError:
+            sys.stderr.write(f"Key '{i}' is not an available conda environment name. The options are: " + ", ".join(environ.keys()))
+            sys.exit(1)
+        with open(f"{outdir}/workflow/envs/{i}.yaml", "w", encoding="utf-8") as recipe:
+            yaml.dump(env_dict, recipe, default_flow_style= False, sort_keys=False, width=float('inf'), indent=2)
+
+    if "spades" in envs:
+        # post-deployment script
+        with open(f"{outdir}/workflow/envs/spades.post-deploy.sh", "w", encoding="utf-8") as shellscript:
+            shellscript.write("wget -O .spades.tar.gz https://github.com/ablab/spades/releases/download/v4.0.0/SPAdes-4.0.0-Linux.tar.gz\n")
+            shellscript.write("tar -xvzf .spades.tar.gz && rm .spades.tar.gz\n")
+            shellscript.write("mv SPAdes-4.0.0-Linux/bin/* ${CONDA_PREFIX}/bin && mv SPAdes-4.0.0-Linux/share/* ${CONDA_PREFIX}/share\n")
+            shellscript.write("rm -r SPAdes-4.0.0-Linux\n")
+
+def check_environments(dirpath: str, envs: list) -> None:
+    """Check that the provided dir exists and contains the necessary environment definitions"""
+    if not os.path.exists(f"{dirpath}/workflow/envs"):
+        print_error("missing conda files", "This working directory does not contain the expected directory of conda environment definitions ([blue bold]workflow/envs/[/blue bold])\n  - use [green bold]--conda[/green bold] to recreate it")
+        sys.exit(1)
+    envlist = os.listdir(f"{dirpath}/workflow/envs")
+    errcount = 0
+    errtable = Table(show_footer=True, box=box.SIMPLE)
+    errtable.add_column("File", justify="left", no_wrap=True)
+    errtable.add_column("Status", justify="center")
+    for i in envs:
+        if f"{i}.yaml" in envlist:
+            errtable.add_row(f"[dim]{i}.yaml", "[dim]present")
+        else:
+            errcount += 1
+            errtable.add_row(f"[yellow bold]{i}.yaml", "[yellow bold]missing")
+    if errcount > 0:
+        print_error("Missing environment files", f"The directory [blue]{dirpath}/workflows/envs[/blue] is missing [yellow bold]{errcount}[/yellow bold] of the expected conda environment definition files.")
+        print_solution_with_culprits(
+            "Check that the names conform to Harpy's expectations, otherwise you can recreate this directory using the [green bold]--conda[/green bold] option.",
+            "Expected environment files:"
+            )
+        rprint(errtable, file = sys.stderr)
+        sys.exit(1)

harpy/_printing.py

@@ -23,7 +23,7 @@ def print_setup_error(exitcode):
         errortext = "Something is wrong with the Snakefile for this workflow. If you manually edited the Snakefile, see the error below for troubleshooting. If you didn't, it's probably a bug (oops!) and you should submit an issue on GitHub: [bold]https://github.com/pdimens/harpy/issues"
         errortype = "Snakefile Error"
     else:
-        errortext = "There was an issue creating the software environment(s) necessary to run this workflow. If you manually edited the conda dependencies in [blue].harpy_envs[/blue], see the error below for troubleshooting. If you didn't, it might be a bug or related to how your system is setup for Conda or Singularity environments and you should submit an issue on GitHub: [bold]https://github.com/pdimens/harpy/issues"
+        errortext = "There was an issue creating the software environment(s) necessary to run this workflow. If you manually edited the conda dependencies in [blue]/workflows/envs[/blue], see the error below for troubleshooting. If you didn't, it might be a bug or related to how your system is setup for Conda or Singularity environments and you should submit an issue on GitHub: [bold]https://github.com/pdimens/harpy/issues"
         errortype = "Software Environment Error"
 
     rprint(

harpy/_validations.py

@@ -32,32 +32,6 @@ def is_plaintext(file_path):
     except UnicodeDecodeError:
         return False
 
-def check_envdir(dirpath):
-    """Check that the provided dir exists and contains the necessary environment definitions"""
-    if not os.path.exists(dirpath):
-        print_error("missing conda files", "This working directory does not contain the expected directory of conda environment definitions ([blue bold].harpy_envs/[/blue bold])\n  - use [green bold]--conda[/green bold] to recreate it")
-        sys.exit(1)
-    envlist = os.listdir(dirpath)
-    envs = ["align", "metassembly", "phase", "qc", "r", "simulations", "stitch", "variants"]
-    errcount = 0
-    errtable = Table(show_footer=True, box=box.SIMPLE)
-    errtable.add_column("File", justify="left", style="blue", no_wrap=True)
-    errtable.add_column("Exists", justify="center")
-    for i in envs:
-        if f"{i}.yaml" in envlist:
-            errtable.add_row(f"{i}.yaml", "[blue]✓")
-        else:
-            errcount += 1
-            errtable.add_row(f"{i}.yaml", "[yellow]🗙")
-    if errcount > 0:
-        print_error("missing conda files", f"The conda environment definition directory ([blue bold]{dirpath}[/blue bold]) is missing [yellow bold]{errcount}[/yellow bold] of the expected definition files. All of the environment files are expected to be present, even if a particular workflow doesn't use it.")
-        print_solution_with_culprits(
-            "Check that the names conform to Harpy's expectations, otheriwse you can recreate this directory using the [green bold]--conda[/green bold] option.",
-            "Expected environment files:"
-            )
-        rprint(errtable, file = sys.stderr)
-        sys.exit(1)
-
 def check_impute_params(parameters):
     """Validate the STITCH parameter file for column names, order, types, missing values, etc."""
     with open(parameters, "r", encoding="utf-8") as paramfile:

harpy/align.py

@@ -113,6 +113,7 @@ def bwa(inputs, output_dir, genome, depth_window, threads, keep_unmapped, extra_
     fetch_report(workflowdir, "align_bxstats.Rmd")
     os.makedirs(f"{output_dir}/logs/snakemake", exist_ok = True)
     sm_log = snakemake_log(output_dir, "align_bwa")
+    conda_envs = ["align", "r", "qc"]
     configs = {
         "workflow" : "align bwa",
         "snakemake_log" : sm_log,
@@ -123,6 +124,7 @@ def bwa(inputs, output_dir, genome, depth_window, threads, keep_unmapped, extra_
         "depth_windowsize" : depth_window,
         **({'extra': extra_params} if extra_params else {}),
         "workflow_call" : command.rstrip(),
+        "conda_environments" : conda_envs,
         "reports" : {
             "skip": skip_reports,
             **({'plot_contigs': contigs} if contigs else {'plot_contigs': "default"}),
@@ -135,7 +137,7 @@ def bwa(inputs, output_dir, genome, depth_window, threads, keep_unmapped, extra_
     with open(os.path.join(workflowdir, 'config.yaml'), "w", encoding="utf-8") as config:
         yaml.dump(configs, config, default_flow_style= False, sort_keys=False, width=float('inf'))
 
-    create_conda_recipes()
+    create_conda_recipes(output_dir, conda_envs)
     if setup_only:
         sys.exit(0)
 
@@ -216,6 +218,8 @@ def ema(inputs, output_dir, platform, barcode_list, fragment_density, genome, de
     fetch_report(workflowdir, "align_bxstats.Rmd")
     os.makedirs(f"{output_dir}/logs/snakemake", exist_ok = True)
     sm_log = snakemake_log(output_dir, "align_ema")
+    conda_envs = ["align", "r", "qc"]
+
     configs = {
         "workflow" : "align ema",
         "snakemake_log" : sm_log,
@@ -228,6 +232,7 @@ def ema(inputs, output_dir, platform, barcode_list, fragment_density, genome, de
         "EMA_bins" : ema_bins,
         **({'extra': extra_params} if extra_params else {}),
         "workflow_call" : command.rstrip(),
+        "conda_environments" : conda_envs,
         "reports" : {
             "skip": skip_reports,
             **({'plot_contigs': contigs} if contigs else {'plot_contigs': "default"}),
@@ -242,7 +247,7 @@ def ema(inputs, output_dir, platform, barcode_list, fragment_density, genome, de
     with open(os.path.join(workflowdir, 'config.yaml'), "w", encoding="utf-8") as config:
         yaml.dump(configs, config, default_flow_style= False, sort_keys=False, width=float('inf'))
 
-    create_conda_recipes()
+    create_conda_recipes(output_dir, conda_envs)
     if setup_only:
         sys.exit(0)
 
@@ -309,6 +314,7 @@ def strobe(inputs, output_dir, genome, read_length, keep_unmapped, depth_window,
     fetch_report(workflowdir, "align_bxstats.Rmd")
     os.makedirs(f"{output_dir}/logs/snakemake", exist_ok = True)
     sm_log = snakemake_log(output_dir, "align_strobe")
+    conda_envs = ["align", "r", "qc"]
     configs = {
         "workflow" : "align strobe",
         "snakemake_log" : sm_log,
@@ -320,6 +326,7 @@ def strobe(inputs, output_dir, genome, read_length, keep_unmapped, depth_window,
         "depth_windowsize" : depth_window,
         **({'extra': extra_params} if extra_params else {}),
         "workflow_call" : command.rstrip(),
+        "conda_environments" : conda_envs,
         "reports" : {
             "skip": skip_reports,
             **({'plot_contigs': contigs} if contigs else {'plot_contigs': "default"}),
@@ -332,7 +339,7 @@ def strobe(inputs, output_dir, genome, read_length, keep_unmapped, depth_window,
     with open(os.path.join(workflowdir, 'config.yaml'), "w", encoding="utf-8") as config:
         yaml.dump(configs, config, default_flow_style= False, sort_keys=False, width=float('inf'))
 
-    create_conda_recipes()
+    create_conda_recipes(output_dir, conda_envs)
     if setup_only:
         sys.exit(0)
 

harpy/assembly.py

@@ -84,6 +84,7 @@ def assembly(fastq_r1, fastq_r2, bx_tag, kmer_length, max_memory, output_dir, ex
     fetch_rule(workflowdir, f"{asm}.smk")
     os.makedirs(f"{output_dir}/logs/snakemake", exist_ok = True)
     sm_log = snakemake_log(output_dir, asm)
+    conda_envs = ["assembly","qc"]
     configs = {
         "workflow" : asm,
         "snakemake_log" : sm_log,
@@ -111,6 +112,7 @@ def assembly(fastq_r1, fastq_r2, bx_tag, kmer_length, max_memory, output_dir, ex
             "minimum_links" : links
         },
         "workflow_call" : command.rstrip(),
+        "conda_environments" : conda_envs,
         "reports" : {
             "skip": skip_reports,
             "organism_type": organism_type
@@ -123,7 +125,7 @@ def assembly(fastq_r1, fastq_r2, bx_tag, kmer_length, max_memory, output_dir, ex
     with open(os.path.join(workflowdir, 'config.yaml'), "w", encoding="utf-8") as config:
         yaml.dump(configs, config, default_flow_style= False, sort_keys=False, width=float('inf'))
 
-    create_conda_recipes()
+    create_conda_recipes(output_dir, conda_envs)
     if setup_only:
         sys.exit(0)
 

harpy/container.py

@@ -15,7 +15,8 @@ def containerize():
     **INTERNAL USE ONLY**. Used to recreate all the conda environments required
     by the workflows and build a dockerfile from that.
     """
-    create_conda_recipes()
+    #TODO MAKE THIS ALL OF THEM
+    create_conda_recipes("container")
     fetch_rule(os.getcwd(), "containerize.smk")
 
     with open("Dockerfile", "w", encoding = "utf-8") as dockerfile:

harpy/deconvolve.py

@@ -64,6 +64,7 @@ def deconvolve(inputs, output_dir, kmer_length, window_size, density, dropout, t
     fetch_rule(workflowdir, "deconvolve.smk")
     os.makedirs(f"{output_dir}/logs/snakemake", exist_ok = True)
     sm_log = snakemake_log(output_dir, "deconvolve")
+    conda_envs = ["qc"]
     configs = {
         "workflow": "deconvolve",
         "snakemake_log" : sm_log,
@@ -73,12 +74,13 @@ def deconvolve(inputs, output_dir, kmer_length, window_size, density, dropout, t
         "density" :  density,
         "dropout" :  dropout,
         "workflow_call" : command.rstrip(),
+        "conda_environments" : conda_envs,
         "inputs": [i.as_posix() for i in fqlist]
         }
     with open(os.path.join(workflowdir, 'config.yaml'), "w", encoding="utf-8") as config:
         yaml.dump(configs, config, default_flow_style= False, sort_keys=False, width=float('inf'))
 
-    create_conda_recipes()
+    create_conda_recipes(output_dir, conda_envs)
     if setup_only:
         sys.exit(0)
 

harpy/demultiplex.py

@@ -39,7 +39,7 @@ def demultiplex():
 }
 
 @click.command(no_args_is_help = True, context_settings=dict(allow_interspersed_args=False), epilog = "Documentation: https://pdimens.github.io/harpy/workflows/demultiplex/")
-@click.option('-s', '--schema', required = True, type=click.Path(exists=True, dir_okay=False, readable=True), help = 'Tab-delimited file of sample\<tab\>barcode')
+@click.option('-s', '--schema', required = True, type=click.Path(exists=True, dir_okay=False, readable=True), help = 'File of `sample`\\<TAB\\>`barcode`')
 @click.option('-t', '--threads', default = 4, show_default = True, type = click.IntRange(min = 1, max_open = True), help = 'Number of threads to use')
 @click.option('-o', '--output-dir', type = click.Path(exists = False), default = "Demultiplex", show_default=True,  help = 'Output directory name')
 @click.option('--conda',  is_flag = True, default = False, help = 'Use conda/mamba instead of a container')
@@ -57,7 +57,7 @@ def gen1(r1_fq, r2_fq, i1_fq, i2_fq, output_dir, schema, threads, snakemake, ski
     Demultiplex Generation I haplotagged FASTQ files
 
     Use the R1, R2, I2, and I2 FASTQ files provided by the sequencing facility as inputs (in that exact order) provided after the options. 
-    The `--schema` must be **tab** (or space) delimited, have **no header** (i.e. no column names), and be in the format of `sample`\<tab\>`barcode`,
+    The `--schema` must be **tab** (or space) delimited, have **no header** (i.e. no column names), and be in the format of `sample`\\<TAB\\>`barcode`,
     where `barcode` is the C- beadtag assigned to the sample (.e.g. `C01`, `C02`, etc.)
     """
     output_dir = output_dir.rstrip("/")
@@ -76,11 +76,13 @@ def gen1(r1_fq, r2_fq, i1_fq, i2_fq, output_dir, schema, threads, snakemake, ski
     fetch_rule(workflowdir, "demultiplex_gen1.smk")
     os.makedirs(f"{output_dir}/logs/snakemake", exist_ok = True)
     sm_log = snakemake_log(output_dir, "demultiplex_gen1")
+    conda_envs = ["qc"]
     configs = {
         "workflow" : "demultiplex gen1",
         "snakemake_log" : sm_log,
         "output_directory" : output_dir,
         "workflow_call" : command.rstrip(),
+        "conda_environments" : conda_envs,
         "reports" : {
             "skip": skip_reports
         },
@@ -95,7 +97,7 @@ def gen1(r1_fq, r2_fq, i1_fq, i2_fq, output_dir, schema, threads, snakemake, ski
     with open(os.path.join(workflowdir, 'config.yaml'), "w", encoding= "utf-8") as config:
         yaml.dump(configs, config, default_flow_style= False, sort_keys=False, width=float('inf'))
 
-    create_conda_recipes()
+        create_conda_recipes(output_dir, conda_envs)
     if setup_only:
         sys.exit(0)