Docs: point to bcbio organization repository

.gitignore

@@ -28,3 +28,4 @@ cwl/*-workflow
 .idea/
 __pycache__
 .coverage
+.pytest_cache

Dockerfile

@@ -12,7 +12,7 @@ RUN apt-get update && \
 # bcbio-nextgen installation
     mkdir -p /tmp/bcbio-nextgen-install && cd /tmp/bcbio-nextgen-install && \
     wget --no-check-certificate \
-      https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py && \
+      https://raw.github.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py && \
     python bcbio_nextgen_install.py /usr/local/share/bcbio-nextgen \
       --isolate --minimize-disk --nodata -u development && \
     git config --global url.https://github.com/.insteadOf git://github.com/ && \
@@ -28,7 +28,7 @@ RUN apt-get update && \
 
 # add user run script
     wget --no-check-certificate -O createsetuser \
-      https://raw.github.com/chapmanb/bcbio-nextgen-vm/master/scripts/createsetuser && \
+      https://raw.github.com/bcbio/bcbio-nextgen-vm/master/scripts/createsetuser && \
     chmod a+x createsetuser && mv createsetuser /sbin && \
 
 # clean filesystem

README.rst

@@ -10,8 +10,8 @@ provides a shared community resource that handles the data processing component
 of sequencing analysis, providing researchers with more time to focus on the
 downstream biology.
 
-.. image:: https://travis-ci.org/chapmanb/bcbio-nextgen.png
-    :target: https://travis-ci.org/chapmanb/bcbio-nextgen
+.. image:: https://travis-ci.org/bcbio/bcbio-nextgen.png
+    :target: https://travis-ci.org/bcbio/bcbio-nextgen
 
 Features
 --------
@@ -55,7 +55,7 @@ Quick start
 
 1. `Install`_ ``bcbio-nextgen`` with all tool dependencies and data files::
 
-         wget https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py
+         wget https://raw.github.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py
          python bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local \
            --genomes GRCh37 --aligners bwa --aligners bowtie2
 
@@ -74,8 +74,8 @@ Quick start
          cd project1/work
          bcbio_nextgen.py ../config/project1.yaml -n 8
 
-.. _system configuration file: https://github.com/chapmanb/bcbio-nextgen/blob/master/config/bcbio_system.yaml
-.. _sample description file: https://github.com/chapmanb/bcbio-nextgen/blob/master/config/bcbio_sample.yaml
+.. _system configuration file: https://github.com/bcbio/bcbio-nextgen/blob/master/config/bcbio_system.yaml
+.. _sample description file: https://github.com/bcbio/bcbio-nextgen/blob/master/config/bcbio_sample.yaml
 .. _Automatically create a processing description: https://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html#automated-sample-configuration
 .. _Install: https://bcbio-nextgen.readthedocs.org/en/latest/contents/installation.html#automated
 .. _configuration options: https://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html
@@ -88,7 +88,7 @@ See the `full documentation`_ and `longer analysis-based articles
 and discussion on the `biovalidation mailing list`_.
 
 .. _full documentation: https://bcbio-nextgen.readthedocs.org
-.. _GitHub: https://github.com/chapmanb/bcbio-nextgen/issues
+.. _GitHub: https://github.com/bcbio/bcbio-nextgen/issues
 .. _biovalidation mailing list: https://groups.google.com/d/forum/biovalidation
 
 Contributors

bcbio/broad/__init__.py

@@ -26,7 +26,7 @@ def get_default_jvm_opts(tmp_dir=None, parallel_gc=False):
     Avoids issues with multiple spun up Java processes running into out of memory errors.
     Parallel GC can use a lot of cores on big machines and primarily helps reduce task latency
     and responsiveness which are not needed for batch jobs.
-    https://github.com/chapmanb/bcbio-nextgen/issues/532#issuecomment-50989027
+    https://github.com/bcbio/bcbio-nextgen/issues/532#issuecomment-50989027
     https://wiki.csiro.au/pages/viewpage.action?pageId=545034311
     http://stackoverflow.com/questions/9738911/javas-serial-garbage-collector-performing-far-better-than-other-garbage-collect
     However, serial GC causes issues with Spark local runs so we use parallel for those cases:

bcbio/install.py

@@ -29,10 +29,10 @@
 from bcbio.pipeline import datadict as dd
 
 REMOTES = {
-    "requirements": "https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements-conda.txt",
-    "gitrepo": "https://github.com/chapmanb/bcbio-nextgen.git",
+    "requirements": "https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/requirements-conda.txt",
+    "gitrepo": "https://github.com/bcbio/bcbio-nextgen.git",
     "cloudbiolinux": "https://github.com/chapmanb/cloudbiolinux/archive/master.tar.gz",
-    "genome_resources": "https://raw.github.com/chapmanb/bcbio-nextgen/master/config/genomes/%s-resources.yaml",
+    "genome_resources": "https://raw.github.com/bcbio/bcbio-nextgen/master/config/genomes/%s-resources.yaml",
     "snpeff_dl_url": ("http://downloads.sourceforge.net/project/snpeff/databases/v{snpeff_ver}/"
                       "snpEff_v{snpeff_ver}_{genome}.zip")}
 SUPPORTED_GENOMES = ["GRCh37", "hg19", "hg38", "hg38-noalt", "mm10", "mm9",

bcbio/pipeline/rnaseq.py

@@ -74,7 +74,7 @@ def run_rnaseq_variant_calling(data):
     if isinstance(variantcaller, list) and len(variantcaller) > 1:
         logger.error("Only one variantcaller can be run for RNA-seq at "
                      "this time. Post an issue here "
-                     "(https://github.com/chapmanb/bcbio-nextgen/issues) "
+                     "(https://github.com/bcbio/bcbio-nextgen/issues) "
                      "if this is something you need to do.")
         sys.exit(1)
 

bcbio/rnaseq/kallisto.py

@@ -30,7 +30,7 @@ def run_kallisto_rnaseq(data):
     assert file_exists(fasta_file), "%s was not found, exiting." % fasta_file
     assert fq2, ("bcbio doesn't support kallisto for single-end reads, we can "
                  "add support for this if you open up an issue about it here: "
-                 "https://github.com/chapmanb/bcbio-nextgen/issues")
+                 "https://github.com/bcbio/bcbio-nextgen/issues")
     out_file = kallisto_rnaseq(fq1, fq2, kallisto_dir, gtf_file, fasta_file, data)
     data = dd.set_kallisto_quant(data, out_file)
     return [[data]]

bcbio/rnaseq/umi.py

@@ -294,7 +294,7 @@ def demultiplex_samples(data):
     files = data["files"]
     if len(files) == 2:
         logger.error("Sample demultiplexing doesn't handle paired-end reads, but "
-            "we can add it. Open an issue here https://github.com/chapmanb/bcbio-nextgen/issues if you need this and we'll add it.")
+            "we can add it. Open an issue here https://github.com/bcbio/bcbio-nextgen/issues if you need this and we'll add it.")
         sys.exit(1)
     else:
         fq1 = files[0]

bcbio/structural/cnvkit.py

@@ -297,7 +297,7 @@ def _cnvkit_segment(cnr_file, cov_interval, data, items, out_file=None):
                 if cov_interval == "genome":
                     cmd += ["--threshold", "0.00001"]
                 # For tumors, remove very low normalized regions, avoiding upcaptured noise
-                # https://github.com/chapmanb/bcbio-nextgen/issues/2171#issuecomment-348333650
+                # https://github.com/bcbio/bcbio-nextgen/issues/2171#issuecomment-348333650
                 paired = vcfutils.get_paired(items)
                 if paired:
                     cmd += ["--drop-low-coverage"]
@@ -407,7 +407,7 @@ def _get_batch_gender(items):
 
     Better not to specify for mixed populations, CNVkit will work
     it out
-    https://github.com/chapmanb/bcbio-nextgen/commit/1a0e217c8a4d3cee10fa890fb3cfd4db5034281d#r26279752
+    https://github.com/bcbio/bcbio-nextgen/commit/1a0e217c8a4d3cee10fa890fb3cfd4db5034281d#r26279752
     """
     genders = set([population.get_gender(x) for x in items])
     if len(genders) == 1:

bcbio/variation/bedutils.py

@@ -23,8 +23,8 @@ def get_sort_cmd(tmp_dir=None):
     This also fixes versions of sort, like 8.22 in CentOS 7.1, that have broken
     sorting without version sorting specified.
 
-    https://github.com/chapmanb/bcbio-nextgen/issues/624
-    https://github.com/chapmanb/bcbio-nextgen/issues/1017
+    https://github.com/bcbio/bcbio-nextgen/issues/624
+    https://github.com/bcbio/bcbio-nextgen/issues/1017
     """
     has_versionsort = subprocess.check_output("sort --help | grep version-sort; exit 0", shell=True).strip()
     if has_versionsort:

bcbio/variation/recalibrate.py

@@ -150,7 +150,7 @@ def _gatk_apply_bqsr(data):
                 params = ["-T", "PrintReads", "-R", dd.get_ref_file(data), "-I", in_file,
                           "-BQSR", data["prep_recal"], "-o", tx_out_file]
             # Avoid problems with intel deflater for GATK 3.8 and GATK4
-            # https://github.com/chapmanb/bcbio-nextgen/issues/2145#issuecomment-343095357
+            # https://github.com/bcbio/bcbio-nextgen/issues/2145#issuecomment-343095357
             if gatk_type == "gatk4":
                 params += ["--jdk-deflater", "--jdk-inflater"]
             elif LooseVersion(broad_runner.gatk_major_version()) > LooseVersion("3.7"):

bcbio/variation/validate.py

@@ -283,7 +283,7 @@ def _pick_best_quality_score(vrn_file):
 
     Implementation based on discussion:
 
-    https://github.com/chapmanb/bcbio-nextgen/commit/a538cecd86c0000d17d3f9d4f8ac9d2da04f9884#commitcomment-14539249
+    https://github.com/bcbio/bcbio-nextgen/commit/a538cecd86c0000d17d3f9d4f8ac9d2da04f9884#commitcomment-14539249
 
     (RTG=AVR/GATK=VQSLOD/MuTect=t_lod_fstar, otherwise GQ, otherwise QUAL, otherwise DP.)
 

bcbio/workflow/template.py

@@ -150,7 +150,7 @@ def name_to_config(template):
         with open(template) as in_handle:
             config = yaml.load(in_handle)
     else:
-        base_url = "https://raw.github.com/chapmanb/bcbio-nextgen/master/config/templates/%s.yaml"
+        base_url = "https://raw.github.com/bcbio/bcbio-nextgen/master/config/templates/%s.yaml"
         try:
             with contextlib.closing(urllib.request.urlopen(base_url % template)) as in_handle:
                 txt_config = in_handle.read()

config/examples/HCC2218-sv-getdata.sh

@@ -6,7 +6,7 @@ set -eu -o pipefail
 
 mkdir -p config
 cd config
-wget -c https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/HCC2218-sv.yaml
+wget -c https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/config/examples/HCC2218-sv.yaml
 cd ../
 
 mkdir -p input

config/examples/NA12878-exome-methodcmp-getdata.sh

@@ -10,7 +10,7 @@ set -eu -o pipefail
 
 mkdir -p config
 cd config
-wget https://raw.github.com/chapmanb/bcbio-nextgen/master/config/examples/NA12878-exome-methodcmp.yaml
+wget https://raw.github.com/bcbio/bcbio-nextgen/master/config/examples/NA12878-exome-methodcmp.yaml
 cd ..
 
 mkdir -p input

config/examples/NA12878-hg38-validate-getdata.sh

@@ -7,7 +7,7 @@ set -eu -o pipefail
 
 mkdir -p config
 cd config
-wget -c https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/NA12878-hg38-validate.yaml
+wget -c https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/config/examples/NA12878-hg38-validate.yaml
 cd ..
 
 mkdir -p input

config/examples/NA12878-sv-getdata.sh

@@ -9,7 +9,7 @@ set -eu -o pipefail
 
 mkdir -p config
 cd config
-wget -c https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/NA12878-sv.yaml
+wget -c https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/config/examples/NA12878-sv.yaml
 cd ..
 
 mkdir -p input

config/examples/NA24385-10x-getdata.sh

@@ -29,7 +29,7 @@ cd ..
 
 mkdir -p config
 cd config
-wget -c https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/NA24385-10x.yaml
+wget -c https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/config/examples/NA24385-10x.yaml
 cd ..
 
 mkdir -p work

config/examples/cancer-giab-na12878-na24385-getdata.sh

@@ -7,7 +7,7 @@ set -eu -o pipefail
 
 mkdir -p config
 cd config
-wget -c https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/cancer-giab-na12878-na24385.yaml
+wget -c https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/config/examples/cancer-giab-na12878-na24385.yaml
 cd ..
 
 base_url=ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/use_cases/mixtures/UMCUTRECHT_NA12878_NA24385_mixture_10052016

config/examples/giab-validate-setup.sh

@@ -9,7 +9,7 @@ set -eu -o pipefail
 
 mkdir -p config
 cd config
-wget -c https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/giab-validate.yaml
+wget -c https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/config/examples/giab-validate.yaml
 cd ..
 
 mkdir -p input

config/examples/rnaseq-seqc-getdata.sh

@@ -7,7 +7,7 @@ df --block-size=G --output='avail' . | sed s/G//g | awk -v req_disk_space=${REQ_
 
 mkdir -p seqc-test/input
 cd seqc-test
-wget --no-check-certificate https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/rnaseq-seqc.yaml
+wget --no-check-certificate https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/config/examples/rnaseq-seqc.yaml
 
 cd input
 for SAMPLE in SRR950078 SRR950079 SRR950080 SRR950081 SRR950082 SRR950083
@@ -16,7 +16,7 @@ do
    wget -O ${SAMPLE}_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR950/${SAMPLE}/${SAMPLE}_2.fastq.gz
 done 
 
-wget --no-check-certificate https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/examples/seqc.csv
+wget --no-check-certificate https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/config/examples/seqc.csv
 
 cd ../
 bcbio_nextgen.py -w template rnaseq-seqc.yaml input/seqc.csv input

config/galaxy/bcbio/variant.xml

@@ -70,6 +70,6 @@ details:
   <help>
 SNP and indel variant calling using `bcbio-nextgen`_.
 
-.. _bcbio-nextgen: https://github.com/chapmanb/bcbio-nextgen
+.. _bcbio-nextgen: https://github.com/bcbio/bcbio-nextgen
   </help>
 </tool>

config/teaching/cancer-syn3-chr6-prep.sh

@@ -11,7 +11,7 @@ rm -f cancer-syn3-chr6-input.tar.gz
 
 mkdir -p config
 cd config
-wget -c https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/config/teaching/cancer-syn3-chr6.yaml
+wget -c https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/config/teaching/cancer-syn3-chr6.yaml
 cd ..
 
 mkdir -p work

docs/contents/citations.rst

@@ -1,19 +1,19 @@
 Citations
 ---------
 
-https://github.com/chapmanb/bcbio-nextgen
+https://github.com/bcbio/bcbio-nextgen
 
 small RNA-seq
 =============
 
-Data was analyzed with bcbio-nextgen (https://github.com/chapmanb/bcbio-nextgen)
+Data was analyzed with bcbio-nextgen (https://github.com/bcbio/bcbio-nextgen)
 using piDNA to detect the adapter, cutadapt to remove it, STAR/bowtie to align against
 the genome and seqcluster to detect small RNA transcripts. miRNAs were detected using
 miraligner tool with miRBase as the reference miRNA database. tRNA profiles were
 detected using tdrmapper tool. mirdeep2 was used for discovery of novel miRNAs. FastQC
 was used for QC metrics and multiqc for reporting.
 
-Download BIB format: https://github.com/chapmanb/bcbio-nextgen/tree/master/docs/contents/misc/bcbio-smallrna.bib
+Download BIB format: https://github.com/bcbio/bcbio-nextgen/tree/master/docs/contents/misc/bcbio-smallrna.bib
 
 Tools
 ~~~~~

docs/contents/cloud.rst

@@ -9,7 +9,7 @@ perform analyses at scale with no investment in local hardware. They also offer
 full programmatic control over the environment, allowing bcbio to automate the
 entire setup, run and teardown process.
 
-`bcbio-vm <https://github.com/chapmanb/bcbio-nextgen-vm>`_ provides a wrapper
+`bcbio-vm <https://github.com/bcbio/bcbio-nextgen-vm>`_ provides a wrapper
 around bcbio-nextgen that automates interaction with AWS and `Docker
 <https://www.docker.com/>`_. ``bcbio_vm.py`` also cleans up the command line
 usage to make it more intuitive and provides a superset of functionality
@@ -284,7 +284,7 @@ And plot, slice, zoom it in an jupyter notebook using matplotlib,
 [highcharts](https://github.com/arnoutaertgeerts/python-highcharts).
 
 In addition to plots, the
-`summarize_timing.py <https://github.com/chapmanb/bcbio-nextgen/blob/master/scripts/utils/summarize_timing.py>`_
+`summarize_timing.py <https://github.com/bcbio/bcbio-nextgen/blob/master/scripts/utils/summarize_timing.py>`_
 utility script prepares a summary table of run times per step.
 
 Shutting down
@@ -312,5 +312,5 @@ that automatically reads and writes these configurations to avoid users needing
 to understand elasticluster internals, but all functionality is fully available.
 Edit your ``~/.bcbio/elasticluster/config`` file to change parameters. You can
 also see the `latest example configuration
-<https://github.com/chapmanb/bcbio-nextgen-vm/blob/master/elasticluster/config>`_.
+<https://github.com/bcbio/bcbio-nextgen-vm/blob/master/elasticluster/config>`_.
 in the bcbio-vm GitHub repository for more details on the other available options.