From 4386025bdb6bc707626934a521819e8ab31cb9d7 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Mon, 18 Mar 2019 22:38:24 -0400
Subject: [PATCH 01/38] add deploy script

---
 deploy.py | 129 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 129 insertions(+)
 create mode 100644 deploy.py

diff --git a/deploy.py b/deploy.py
new file mode 100644
index 000000000..2f993a4bb
--- /dev/null
+++ b/deploy.py
@@ -0,0 +1,129 @@
+import os
+import tempfile
+import argparse
+import subprocess as sp
+import datetime
+import json
+
+HERE = os.path.dirname(__file__)
+
+usage = """
+This script assists in the deployment of lcdb-wf to working directories.
+
+The lcdb-wf repository contains infrastructure for testing that is not
+typically needed when using it in practice. Furthermore, you might not need all
+possible workflows.
+
+This script copies over only the files requred for each "flavor" of analysis
+(rnaseq, chipseq, colocalization, full) and also stores a file,
+`.lcdb-wf-deployment.yaml`, containing details about the git commit that was
+used and the timestamp. This can be used to compare changes and stay
+up-to-date.
+"""
+
+ap = argparse.ArgumentParser(usage=usage)
+ap.add_argument('--flavor', default='full', help='''Options are rnaseq, chipseq, colocalization, full. Default is full.''')
+ap.add_argument('--dest', help='''Destination directory in which to copy files''')
+args = ap.parse_args()
+dest = args.dest
+flavor = args.flavor
+
+flavors = {
+    'all': {
+        'include': [
+            'wrappers/wrappers',
+            'include',
+            'lib',
+            'requirements.txt',
+        ],
+        'exclude': [
+            'wrappers/wrappers/demo',
+            'workflows/*/run_test.sh',
+
+            # The following files to exclude are those that are created from
+            # a test run.
+            'lib/__pycache__',
+            'lib/postprocess/__pycache__',
+            'include/AnnotationHubCache',
+            'workflows/*/Snakefile.test',
+            'workflows/*/references_data',
+            'workflows/*/.snakemake',
+            'workflows/*/data',
+            'workflows/rnaseq/downstream/rnaseq_cache',
+            'workflows/rnaseq/downstream/rnaseq_files',
+            'workflows/rnaseq/downstream/final_clusters',
+            'workflows/rnaseq/downstream/*.tsv*',
+            'workflows/rnaseq/downstream/*log',
+            'workflows/rnaseq/downstream/*html',
+            'workflows/colocalization/results',
+        ],
+    },
+    'chipseq': [
+        'workflows/chipseq',
+        'workflows/references',
+    ],
+    'rnaseq': [
+        'workflows/rnaseq',
+        'workflows/rnaseq/downstream/',
+        'workflows/references',
+    ],
+    'colocalization': [
+        'workflows/colocalization',
+    ],
+
+    'full': [
+        'workflows',
+    ],
+}
+
+paths = set(flavors['all']['include'])
+paths = paths | set(flavors[flavor])
+
+exclude = tempfile.NamedTemporaryFile(delete=False).name
+with open(exclude, 'w') as fout:
+    fout.write('\n'.join(flavors['all']['exclude']))
+
+include = tempfile.NamedTemporaryFile(delete=False).name
+with open(include, 'w') as fout:
+    fout.write('\n'.join(paths) + '\n')
+
+
+sp.check_call([
+    'rsync',
+    '--relative',
+    '-ar',
+    '--files-from={}'.format(include),
+    '--exclude-from={}'.format(exclude),
+    HERE,
+    dest])
+
+
+commit, message = sp.check_output(
+    ['git', 'log', '--oneline', '-1'],
+    universal_newlines=True
+).strip().split(' ', 1)
+now = datetime.datetime.strftime(datetime.datetime.now(), '%Y%m%d%H%M')
+remotes = sp.check_output(
+    ['git', 'remote', '-v'],
+    universal_newlines=True
+)
+remotes = [i.strip() for i in remotes.splitlines()]
+branch = sp.check_output([
+    'git', 'branch'], universal_newlines=True)
+branch = [i for i in branch.splitlines() if i.startswith('*')]
+assert len(branch) == 1
+branch = branch[0]
+branch = branch.split('* ')[1]
+
+d = {
+    'git': {
+        'commit': commit,
+        'message': message,
+        'remotes': remotes,
+        'branch': branch,
+    },
+    'timestamp': now}
+log = os.path.join(dest, '.lcdb-wf-deployment.json')
+with open(log, 'w') as fout:
+    fout.write(json.dumps(d) + '\n')
+os.chmod(log, 0o440)

From ead86b0a782bb362520d8889c7313d65a57e952e Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Mon, 18 Mar 2019 22:38:50 -0400
Subject: [PATCH 02/38] update docs about missing lcdblib and new deploy script

---
 docs/deploy.rst          | 34 ++++++++++++++++++++++++++++++++++
 docs/getting-started.rst | 19 ++++++++++++-------
 docs/index.rst           |  1 +
 3 files changed, 47 insertions(+), 7 deletions(-)
 create mode 100644 docs/deploy.rst

diff --git a/docs/deploy.rst b/docs/deploy.rst
new file mode 100644
index 000000000..da8bc9ac9
--- /dev/null
+++ b/docs/deploy.rst
@@ -0,0 +1,34 @@
+Deploying ``lcdb-wf`` and staying up-to-date
+============================================
+The repository comes with lots of infrastructure for testing that is not
+necessarily needed in practice when using lcdb-wf for a project. To get
+a simplified version:
+
+.. code-block:: bash
+
+   python deploy.py --flavor rnaseq project-dir
+
+
+The script will use ``rsync`` to copy over files to `project-dir`, excluding
+various test files and excluding any files that may have been created in the
+process of testing. For "flavor", choose ``chipseq``, ``rnaseq``,
+``colocalization``, or ``full`` to get everything. 
+
+This script also writes a file in the destination called
+``.lcdb-wf-deployment.json`` which stores details about what commit was used to
+deploy and the timestamp. This can come in handy later when comparing
+a deployed directory with the main repository to decide whether to update.
+
+Updating
+--------
+The most straightforward approach to updating is to use a diff tool like `meld
+<http://meldmerge.org>`_ to visually compare differences between a deployed
+project and a freshly-cloned version of lcdb-wf:
+
+.. code-block:: bash
+
+   git clone https://github.com/lcdb/lcdb-wf.git comparison-directory
+   meld project-dir comparison-directory
+
+This way you can pick and choose which updates are relevant without having to
+resort to arcane git commands and difficult merges.
diff --git a/docs/getting-started.rst b/docs/getting-started.rst
index d7e40d923..b155ac9cc 100644
--- a/docs/getting-started.rst
+++ b/docs/getting-started.rst
@@ -29,10 +29,9 @@ Otherwise, install `Miniconda <https://conda.io/miniconda.html>`_.
 
 .. code-block:: bash
 
-    conda config --add channels lcdb
     conda config --add channels defaults
-    conda config --add channels conda-forge
     conda config --add channels bioconda
+    conda config --add channels conda-forge
 
 
 Setup required once per project
@@ -77,11 +76,7 @@ use anything. Note that here we specify the channels to use, which include
 
 ::
 
-    conda create -n lcdb-wf \
-      --file requirements.txt \
-      --channel bioconda \
-      --channel conda-forge \
-      --channel lcdb
+    conda create -n lcdb-wf --file requirements.txt
 
 Then activate the environment::
 
@@ -93,6 +88,16 @@ You might want to hold off on this for now if you'll be running the tests::
 
     source deactivate
 
+.. note::
+
+   An alternative approach is to create an environment at a specific path, for
+   example inside a project directory:
+
+   .. code-block:: bash
+
+       conda create -p ./env --file requirements.txt
+       source activate ./env
+
 Next steps
 ----------
 
diff --git a/docs/index.rst b/docs/index.rst
index 861b88f3e..f19efd245 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -89,6 +89,7 @@ See :ref:`getting-started` to get started.
 
    getting-started
    tests
+   deploy
    workflows
    config
    references

From 583a39d090bda5ec1ea5bb0b183a1a2fc7e38cb4 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Mon, 18 Mar 2019 22:41:35 -0400
Subject: [PATCH 03/38] update changelog

---
 docs/changelog.rst | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/docs/changelog.rst b/docs/changelog.rst
index 4059694c7..5e766c623 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -4,6 +4,14 @@ Changelog
 Changes since v1.2
 ------------------
 
+Infrastructure
+~~~~~~~~~~~~~~
+- new deploy script to copy over only the files necessary for an analysis,
+  avoiding the clutter of testing infrastructure.
+- lcdblib, an external package, is no longer a dependency. In the interest of
+  transparency, the relevant code was copied over to the ``lib`` directory in
+  this repository.
+
 ChIP-seq and RNA-seq
 ~~~~~~~~~~~~~~~~~~~~
 
@@ -236,4 +244,4 @@ Both RNA-seq and ChIP-seq
 
 v1.0
 ----
-First full release.
\ No newline at end of file
+First full release.

From 9c012f595f8799bc689860bd8f8005779767cb13 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 10:44:07 -0400
Subject: [PATCH 04/38] add task to print environment

---
 .circleci/config.yml | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index d1ceee31d..f95c8911f 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -217,6 +217,19 @@ jobs:
           name: Build and upload docs
           command: ci/build-docs.sh
 
+  report-env:
+    <<: *defaults
+    steps:
+      - add_ssh_keys:
+          fingerprints:
+            - 99:b4:dd:2c:82:9a:27:07:ca:b4:eb:bf:9c:49:4a:72
+      - checkout
+      - *restore_cache
+      - *set-path
+      - run:
+          name: Report environment
+          command: conda env export -n lcdb-wf-test
+
 
 workflows:
   version: 2
@@ -269,3 +282,15 @@ workflows:
       - build-docs:
           requires:
             - initial-setup
+
+      - report-env:
+          requires:
+            - rnaseq
+            - rnaseq-star
+            - chipseq
+            - references
+            - colocalization
+          filters:
+            branches:
+              ignore:
+                - master

From 0049bfef452489efb7acc35c2ba72d359ba2903a Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 11:08:16 -0400
Subject: [PATCH 05/38] rm lcdb channel; fix channel order

---
 .circleci/setup.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.circleci/setup.sh b/.circleci/setup.sh
index 0e372b7cf..fd13e1b8b 100755
--- a/.circleci/setup.sh
+++ b/.circleci/setup.sh
@@ -27,9 +27,8 @@ if ! type conda > /dev/null; then
     bash miniconda.sh -b -p $WORKSPACE/miniconda
 
     conda config --system --add channels defaults
-    conda config --system --add channels conda-forge
     conda config --system --add channels bioconda
-    conda config --system --add channels lcdb
+    conda config --system --add channels conda-forge
 
     # After SSHing in, for some reason this seems to fix it...
     conda install -y r-base=3.4.1 bioconductor-genomeinfodbdata bioconductor-annotationhub

From d2fb1f4638c45cc5dab5e072c8270283e736c241 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 11:08:51 -0400
Subject: [PATCH 06/38] update reqs to trigger rebuild

---
 requirements.txt | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/requirements.txt b/requirements.txt
index 9f5486176..c6c4b35ab 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -17,8 +17,10 @@ cutadapt
 deeptools >=3.0.1
 fastqc
 fastq-screen
+
 # for fastqc running on circleci
 font-ttf-dejavu-sans-mono
+
 gat
 gffutils >=0.8.7.1
 ghostscript

From 1803388a36dbcf4bf479176f7e28f5e1971a520c Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 11:30:30 -0400
Subject: [PATCH 07/38] disable circleci on this branch

---
 .circleci/config.yml | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index f95c8911f..67e82f1d6 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -239,6 +239,10 @@ workflows:
       - pytest:
          requires:
            - initial-setup
+         filters:
+           branches:
+             ignore:
+               - gitlab-runner-config
       - chipseq:
          requires:
            - initial-setup
@@ -246,7 +250,7 @@ workflows:
          filters:
            branches:
              ignore:
-               - master
+               - gitlab-runner-config
       - rnaseq:
           requires:
             - initial-setup
@@ -254,7 +258,7 @@ workflows:
           filters:
             branches:
               ignore:
-                - master
+                - gitlab-runner-config
       - rnaseq-star:
           requires:
             - initial-setup
@@ -262,7 +266,7 @@ workflows:
           filters:
             branches:
               ignore:
-                - master
+                - gitlab-runner-config
       - references:
           requires:
             - initial-setup
@@ -270,7 +274,7 @@ workflows:
           filters:
             branches:
               ignore:
-                - master
+                - gitlab-runner-config
       - colocalization:
           requires:
             - initial-setup
@@ -278,7 +282,7 @@ workflows:
           filters:
             branches:
               ignore:
-                - master
+                - gitlab-runner-config
       - build-docs:
           requires:
             - initial-setup
@@ -293,4 +297,4 @@ workflows:
           filters:
             branches:
               ignore:
-                - master
+                - gitlab-runner-config

From 92a2d64257972a17e33a56614296f5cadeccc6e2 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 11:32:23 -0400
Subject: [PATCH 08/38] disable intial setup as well

---
 .circleci/config.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 67e82f1d6..e09514f46 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -235,7 +235,11 @@ workflows:
   version: 2
   test-suite:
     jobs:
-      - initial-setup
+      - initial-setup:
+         filters:
+           branches:
+             ignore:
+               - gitlab-runner-config
       - pytest:
          requires:
            - initial-setup

From 588745a383b1a0a33994e66ff0762c08694dff3f Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 11:36:06 -0400
Subject: [PATCH 09/38] add test install script

---
 .circleci/setup.sh | 9 +++------
 .gitlab-ci.yml     | 2 ++
 2 files changed, 5 insertions(+), 6 deletions(-)
 create mode 100644 .gitlab-ci.yml

diff --git a/.circleci/setup.sh b/.circleci/setup.sh
index fd13e1b8b..8bf5b7662 100755
--- a/.circleci/setup.sh
+++ b/.circleci/setup.sh
@@ -2,11 +2,11 @@
 set -e
 
 WORKSPACE=`pwd`
-MINICONDA_VER=4.3.21
+MINICONDA_VER=latest
 
 # Set path
-echo "export PATH=$WORKSPACE/miniconda/bin:$PATH" >> $BASH_ENV
-source $BASH_ENV
+echo "export PATH=$WORKSPACE/miniconda/bin:$PATH" >> ~/.bashrc
+source ~/.bashrc
 
 if ! type conda > /dev/null; then
     echo "Setting up conda..."
@@ -31,11 +31,8 @@ if ! type conda > /dev/null; then
     conda config --system --add channels conda-forge
 
     # After SSHing in, for some reason this seems to fix it...
-    conda install -y r-base=3.4.1 bioconductor-genomeinfodbdata bioconductor-annotationhub
     conda update -y conda
     conda create -n lcdb-wf-test -y --file requirements.txt
-    conda remove -y r-base
 
-    yum install -y git
 fi
 
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 000000000..629636705
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,2 @@
+job:
+  script: "bash .circleci/setup.sh"

From e185d2c33df6280f488b2069d0ca5d5e6250c858 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 13:34:24 -0400
Subject: [PATCH 10/38] try caching

---
 .gitlab-ci.yml | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 629636705..815bd14c8 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,2 +1,22 @@
-job:
+
+initialize-conda:
   script: "bash .circleci/setup.sh"
+  image: "debian:latest"
+  cache:
+    key: "$(md5sum requirements.txt | cut -f1 -d ' ')"
+    paths:
+      - "miniconda"
+    policy: "push"
+
+run-chipseq:
+  script:
+    - source activate lcdb-wf-test
+    - python ci/get-data.py
+    - cd workflows/chipseq
+    - ./run_test.sh -n
+  cache:
+    key: "$(md5sum requirements.txt | cut -f1 -d ' ')"
+    paths:
+      - "miniconda"
+    policy: "pull"
+

From 9cf95ee6eca903e3a32941a2912fb132bd92a057 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 13:37:36 -0400
Subject: [PATCH 11/38] install curl

---
 .circleci/setup.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.circleci/setup.sh b/.circleci/setup.sh
index 8bf5b7662..ded00941a 100755
--- a/.circleci/setup.sh
+++ b/.circleci/setup.sh
@@ -4,6 +4,8 @@ set -e
 WORKSPACE=`pwd`
 MINICONDA_VER=latest
 
+sudo apt-get install curl
+
 # Set path
 echo "export PATH=$WORKSPACE/miniconda/bin:$PATH" >> ~/.bashrc
 source ~/.bashrc

From 2ab5f2b85b3a02ea738c6846949f0555a06bd7e9 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 13:38:45 -0400
Subject: [PATCH 12/38] use steps

---
 .gitlab-ci.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 815bd14c8..7c3f9b58b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,7 +1,11 @@
+steps:
+  - init
+  - workflows
 
 initialize-conda:
-  script: "bash .circleci/setup.sh"
+  step: "init"
   image: "debian:latest"
+  script: "bash .circleci/setup.sh"
   cache:
     key: "$(md5sum requirements.txt | cut -f1 -d ' ')"
     paths:
@@ -9,6 +13,8 @@ initialize-conda:
     policy: "push"
 
 run-chipseq:
+  step: "workflows"
+  image: "debian:latest"
   script:
     - source activate lcdb-wf-test
     - python ci/get-data.py

From 0ba5f86c54a10187349fe16975aebc5d2b7ddee4 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 13:40:11 -0400
Subject: [PATCH 13/38] s/step/stage

---
 .gitlab-ci.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7c3f9b58b..f9d6ab1e3 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,9 +1,9 @@
-steps:
+stages:
   - init
   - workflows
 
 initialize-conda:
-  step: "init"
+  stage: "init"
   image: "debian:latest"
   script: "bash .circleci/setup.sh"
   cache:
@@ -13,7 +13,7 @@ initialize-conda:
     policy: "push"
 
 run-chipseq:
-  step: "workflows"
+  stage: "workflows"
   image: "debian:latest"
   script:
     - source activate lcdb-wf-test

From f31228e179bb44e71272af619334165bd98d9cf4 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 13:41:22 -0400
Subject: [PATCH 14/38] no sudo

---
 .circleci/setup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/setup.sh b/.circleci/setup.sh
index ded00941a..9124b40fb 100755
--- a/.circleci/setup.sh
+++ b/.circleci/setup.sh
@@ -4,7 +4,7 @@ set -e
 WORKSPACE=`pwd`
 MINICONDA_VER=latest
 
-sudo apt-get install curl
+apt-get install curl
 
 # Set path
 echo "export PATH=$WORKSPACE/miniconda/bin:$PATH" >> ~/.bashrc

From defa967c2008b12741f2f1ce304f69a68f8b08d6 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 13:50:12 -0400
Subject: [PATCH 15/38] install curl

---
 .circleci/setup.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.circleci/setup.sh b/.circleci/setup.sh
index 9124b40fb..dd6ef0126 100755
--- a/.circleci/setup.sh
+++ b/.circleci/setup.sh
@@ -4,7 +4,8 @@ set -e
 WORKSPACE=`pwd`
 MINICONDA_VER=latest
 
-apt-get install curl
+apt-get upate
+apt-get install -y curl
 
 # Set path
 echo "export PATH=$WORKSPACE/miniconda/bin:$PATH" >> ~/.bashrc

From 720ae8355d5c848fe3e7abe793bc37436d679b3b Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 13:51:09 -0400
Subject: [PATCH 16/38] install curl

---
 .circleci/setup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/setup.sh b/.circleci/setup.sh
index dd6ef0126..4efb0aa51 100755
--- a/.circleci/setup.sh
+++ b/.circleci/setup.sh
@@ -4,7 +4,7 @@ set -e
 WORKSPACE=`pwd`
 MINICONDA_VER=latest
 
-apt-get upate
+apt-get update
 apt-get install -y curl
 
 # Set path

From bc5f90d232be7dd824096e83661e028c141305f9 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 13:55:58 -0400
Subject: [PATCH 17/38] s/debian/ubuntu/

---
 .gitlab-ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f9d6ab1e3..96df418ec 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,7 +4,7 @@ stages:
 
 initialize-conda:
   stage: "init"
-  image: "debian:latest"
+  image: "ubuntu:latest"
   script: "bash .circleci/setup.sh"
   cache:
     key: "$(md5sum requirements.txt | cut -f1 -d ' ')"
@@ -14,7 +14,7 @@ initialize-conda:
 
 run-chipseq:
   stage: "workflows"
-  image: "debian:latest"
+  image: "ubuntu:latest"
   script:
     - source activate lcdb-wf-test
     - python ci/get-data.py

From d796dd278606ca6c32570313e61372ffee292c69 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 13:59:46 -0400
Subject: [PATCH 18/38] always install

---
 .circleci/setup.sh | 48 +++++++++++++++++++++-------------------------
 1 file changed, 22 insertions(+), 26 deletions(-)

diff --git a/.circleci/setup.sh b/.circleci/setup.sh
index 4efb0aa51..5cac5e7c3 100755
--- a/.circleci/setup.sh
+++ b/.circleci/setup.sh
@@ -11,31 +11,27 @@ apt-get install -y curl
 echo "export PATH=$WORKSPACE/miniconda/bin:$PATH" >> ~/.bashrc
 source ~/.bashrc
 
-if ! type conda > /dev/null; then
-    echo "Setting up conda..."
-
-    # setup conda if not loaded from cache
-    mkdir -p $WORKSPACE
-
-    # step 1: download and install miniconda
-    if [[ $OSTYPE == darwin* ]]; then
-        tag="MacOSX"
-    elif [[ $OSTYPE == linux* ]]; then
-        tag="Linux"
-    else
-        echo "Unsupported OS: $OSTYPE"
-        exit 1
-    fi
-    curl -L -o miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-$MINICONDA_VER-$tag-x86_64.sh
-    bash miniconda.sh -b -p $WORKSPACE/miniconda
-
-    conda config --system --add channels defaults
-    conda config --system --add channels bioconda
-    conda config --system --add channels conda-forge
-
-    # After SSHing in, for some reason this seems to fix it...
-    conda update -y conda
-    conda create -n lcdb-wf-test -y --file requirements.txt
-
+echo "Setting up conda..."
+
+# setup conda if not loaded from cache
+mkdir -p $WORKSPACE
+
+# step 1: download and install miniconda
+if [[ $OSTYPE == darwin* ]]; then
+    tag="MacOSX"
+elif [[ $OSTYPE == linux* ]]; then
+    tag="Linux"
+else
+    echo "Unsupported OS: $OSTYPE"
+    exit 1
 fi
+curl -L -o miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-$MINICONDA_VER-$tag-x86_64.sh
+bash miniconda.sh -b -p $WORKSPACE/miniconda
+
+conda config --system --add channels defaults
+conda config --system --add channels bioconda
+conda config --system --add channels conda-forge
 
+# After SSHing in, for some reason this seems to fix it...
+conda update -y conda
+conda create -n lcdb-wf-test -y --file requirements.txt

From 115f3a8ec47489b38c933448d1f816075a77b163 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 14:38:00 -0400
Subject: [PATCH 19/38] simplify setup

---
 .circleci/setup.sh | 22 +++++-----------------
 1 file changed, 5 insertions(+), 17 deletions(-)

diff --git a/.circleci/setup.sh b/.circleci/setup.sh
index 5cac5e7c3..76996e6ca 100755
--- a/.circleci/setup.sh
+++ b/.circleci/setup.sh
@@ -3,31 +3,19 @@ set -e
 
 WORKSPACE=`pwd`
 MINICONDA_VER=latest
+tag="Linux"
 
 apt-get update
 apt-get install -y curl
 
 # Set path
-echo "export PATH=$WORKSPACE/miniconda/bin:$PATH" >> ~/.bashrc
-source ~/.bashrc
-
-echo "Setting up conda..."
-
-# setup conda if not loaded from cache
-mkdir -p $WORKSPACE
-
-# step 1: download and install miniconda
-if [[ $OSTYPE == darwin* ]]; then
-    tag="MacOSX"
-elif [[ $OSTYPE == linux* ]]; then
-    tag="Linux"
-else
-    echo "Unsupported OS: $OSTYPE"
-    exit 1
-fi
 curl -L -o miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-$MINICONDA_VER-$tag-x86_64.sh
 bash miniconda.sh -b -p $WORKSPACE/miniconda
 
+echo "export PATH=$WORKSPACE/miniconda/bin:$PATH" >> ~/.bashrc
+source ~/.bashrc
+echo $PATH
+
 conda config --system --add channels defaults
 conda config --system --add channels bioconda
 conda config --system --add channels conda-forge

From 0adbe0a57c03f99e72136be98342ee64b4a94865 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 14:43:35 -0400
Subject: [PATCH 20/38] avoid using ~

---
 .circleci/setup.sh | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.circleci/setup.sh b/.circleci/setup.sh
index 76996e6ca..534652634 100755
--- a/.circleci/setup.sh
+++ b/.circleci/setup.sh
@@ -12,9 +12,11 @@ apt-get install -y curl
 curl -L -o miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-$MINICONDA_VER-$tag-x86_64.sh
 bash miniconda.sh -b -p $WORKSPACE/miniconda
 
-echo "export PATH=$WORKSPACE/miniconda/bin:$PATH" >> ~/.bashrc
-source ~/.bashrc
+set -x
+echo "export PATH=$WORKSPACE/miniconda/bin:$PATH" >> $WORKSPACE/.bashrc
+source $WORKSPACE/.bashrc
 echo $PATH
+set +x
 
 conda config --system --add channels defaults
 conda config --system --add channels bioconda

From 0398ac326134757dd1e5ffe9b6c61e092497b344 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Tue, 19 Mar 2019 16:52:29 -0400
Subject: [PATCH 21/38] global path

---
 .circleci/setup.sh | 9 ++-------
 .gitlab-ci.yml     | 3 +++
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/.circleci/setup.sh b/.circleci/setup.sh
index 534652634..466595bcb 100755
--- a/.circleci/setup.sh
+++ b/.circleci/setup.sh
@@ -1,7 +1,6 @@
 #!/bin/bash
 set -e
 
-WORKSPACE=`pwd`
 MINICONDA_VER=latest
 tag="Linux"
 
@@ -10,13 +9,9 @@ apt-get install -y curl
 
 # Set path
 curl -L -o miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-$MINICONDA_VER-$tag-x86_64.sh
-bash miniconda.sh -b -p $WORKSPACE/miniconda
+bash miniconda.sh -b -p /miniconda
 
-set -x
-echo "export PATH=$WORKSPACE/miniconda/bin:$PATH" >> $WORKSPACE/.bashrc
-source $WORKSPACE/.bashrc
-echo $PATH
-set +x
+export PATH=/miniconda/bin:$PATH
 
 conda config --system --add channels defaults
 conda config --system --add channels bioconda
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 96df418ec..8947c1968 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -2,6 +2,9 @@ stages:
   - init
   - workflows
 
+before_script:
+  - export PATH="/miniconda/bin:$PATH"
+
 initialize-conda:
   stage: "init"
   image: "ubuntu:latest"

From b29f5b29978e3bf0847af00f695270679d85a9c0 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Wed, 20 Mar 2019 16:07:31 -0400
Subject: [PATCH 22/38] show path

---
 .gitlab-ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8947c1968..fbf8a3bf3 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -19,6 +19,7 @@ run-chipseq:
   stage: "workflows"
   image: "ubuntu:latest"
   script:
+    - echo $PATH
     - source activate lcdb-wf-test
     - python ci/get-data.py
     - cd workflows/chipseq

From 018be90d1d6d27109ca249ce21c491eaa9f91101 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Wed, 20 Mar 2019 16:07:47 -0400
Subject: [PATCH 23/38] which conda

---
 .gitlab-ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index fbf8a3bf3..efbee93df 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -20,6 +20,7 @@ run-chipseq:
   image: "ubuntu:latest"
   script:
     - echo $PATH
+    - which conda
     - source activate lcdb-wf-test
     - python ci/get-data.py
     - cd workflows/chipseq

From a202263ea1a277e48bac767c2e0ae6b0b76ea5bd Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 22 Mar 2019 09:06:30 -0400
Subject: [PATCH 24/38] change cache location

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index efbee93df..e94031e5e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -12,7 +12,7 @@ initialize-conda:
   cache:
     key: "$(md5sum requirements.txt | cut -f1 -d ' ')"
     paths:
-      - "miniconda"
+      - "/miniconda"
     policy: "push"
 
 run-chipseq:

From 9b7214c7aeb601e911582b1f1d370093ab9bdf1e Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 22 Mar 2019 09:32:02 -0400
Subject: [PATCH 25/38] cache key

---
 .gitlab-ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index e94031e5e..6529305bf 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -10,7 +10,7 @@ initialize-conda:
   image: "ubuntu:latest"
   script: "bash .circleci/setup.sh"
   cache:
-    key: "$(md5sum requirements.txt | cut -f1 -d ' ')"
+    key: "v1"
     paths:
       - "/miniconda"
     policy: "push"
@@ -26,7 +26,7 @@ run-chipseq:
     - cd workflows/chipseq
     - ./run_test.sh -n
   cache:
-    key: "$(md5sum requirements.txt | cut -f1 -d ' ')"
+    key: "v1"
     paths:
       - "miniconda"
     policy: "pull"

From d48a58daec55caaa2fcdedd6a25f157f4c8edf83 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 22 Mar 2019 09:52:15 -0400
Subject: [PATCH 26/38] fix cache

---
 .gitlab-ci.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6529305bf..8cda9a802 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -20,6 +20,7 @@ run-chipseq:
   image: "ubuntu:latest"
   script:
     - echo $PATH
+    - ls /miniconda/bin
     - which conda
     - source activate lcdb-wf-test
     - python ci/get-data.py
@@ -28,6 +29,6 @@ run-chipseq:
   cache:
     key: "v1"
     paths:
-      - "miniconda"
+      - "/miniconda"
     policy: "pull"
 

From ce9c235690776a0ac135642540e3a21476150902 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
Date: Fri, 22 Mar 2019 11:36:25 -0400
Subject: [PATCH 27/38] add trailing "/" to cache dir

---
 .gitlab-ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8cda9a802..186be7d66 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -12,7 +12,7 @@ initialize-conda:
   cache:
     key: "v1"
     paths:
-      - "/miniconda"
+      - "/miniconda/"
     policy: "push"
 
 run-chipseq:
@@ -29,6 +29,6 @@ run-chipseq:
   cache:
     key: "v1"
     paths:
-      - "/miniconda"
+      - "/miniconda/"
     policy: "pull"
 

From dada0dd73b08a66d648f40800f3f4055b6c76b34 Mon Sep 17 00:00:00 2001
From: Ryan Dale <dalerr@niddk.nih.gov>
Date: Sat, 13 Apr 2019 22:35:06 +0000
Subject: [PATCH 28/38] try different cache dir

---
 .circleci/setup.sh | 4 ++--
 .gitlab-ci.yml     | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.circleci/setup.sh b/.circleci/setup.sh
index 466595bcb..ce6f8924d 100755
--- a/.circleci/setup.sh
+++ b/.circleci/setup.sh
@@ -9,9 +9,9 @@ apt-get install -y curl
 
 # Set path
 curl -L -o miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-$MINICONDA_VER-$tag-x86_64.sh
-bash miniconda.sh -b -p /miniconda
+bash miniconda.sh -b -p $CI_PROJECT_DIR/miniconda
 
-export PATH=/miniconda/bin:$PATH
+export PATH=$CI_PROJECT_DIR/miniconda/bin:$PATH
 
 conda config --system --add channels defaults
 conda config --system --add channels bioconda
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 186be7d66..d47666959 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -3,7 +3,7 @@ stages:
   - workflows
 
 before_script:
-  - export PATH="/miniconda/bin:$PATH"
+  - export PATH="$CI_PROJECT_DIR/miniconda/bin:$PATH"
 
 initialize-conda:
   stage: "init"
@@ -12,7 +12,7 @@ initialize-conda:
   cache:
     key: "v1"
     paths:
-      - "/miniconda/"
+      - "miniconda/"
     policy: "push"
 
 run-chipseq:
@@ -29,6 +29,6 @@ run-chipseq:
   cache:
     key: "v1"
     paths:
-      - "/miniconda/"
+      - "miniconda/"
     policy: "pull"
 

From 913e1b13f3fdd0ef08d1ba681670fc4e307472c9 Mon Sep 17 00:00:00 2001
From: Ryan Dale <dalerr@niddk.nih.gov>
Date: Sun, 14 Apr 2019 19:17:16 +0000
Subject: [PATCH 29/38] be clear about path

---
 .gitlab-ci.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d47666959..608736222 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -12,7 +12,7 @@ initialize-conda:
   cache:
     key: "v1"
     paths:
-      - "miniconda/"
+      - "$CI_PROJECT_DIR/miniconda/"
     policy: "push"
 
 run-chipseq:
@@ -20,7 +20,6 @@ run-chipseq:
   image: "ubuntu:latest"
   script:
     - echo $PATH
-    - ls /miniconda/bin
     - which conda
     - source activate lcdb-wf-test
     - python ci/get-data.py
@@ -29,6 +28,6 @@ run-chipseq:
   cache:
     key: "v1"
     paths:
-      - "miniconda/"
+      - "$CI_PROJECT_DIR/miniconda/"
     policy: "pull"
 

From 8315bb33affca005fe50f827ea6fec2a50011398 Mon Sep 17 00:00:00 2001
From: Ryan Dale <dalerr@niddk.nih.gov>
Date: Sun, 14 Apr 2019 19:43:36 +0000
Subject: [PATCH 30/38] change cache policy

---
 .gitlab-ci.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 608736222..7bafe13d1 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -13,7 +13,6 @@ initialize-conda:
     key: "v1"
     paths:
       - "$CI_PROJECT_DIR/miniconda/"
-    policy: "push"
 
 run-chipseq:
   stage: "workflows"

From 226826d9626680a254d4e84664fbaeadbca2f7ac Mon Sep 17 00:00:00 2001
From: Ryan Dale <dalerr@niddk.nih.gov>
Date: Sun, 14 Apr 2019 20:31:57 +0000
Subject: [PATCH 31/38] do not install if miniconda exists

---
 .circleci/setup.sh | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/.circleci/setup.sh b/.circleci/setup.sh
index ce6f8924d..944a1954a 100755
--- a/.circleci/setup.sh
+++ b/.circleci/setup.sh
@@ -6,10 +6,10 @@ tag="Linux"
 
 apt-get update
 apt-get install -y curl
-
-# Set path
-curl -L -o miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-$MINICONDA_VER-$tag-x86_64.sh
-bash miniconda.sh -b -p $CI_PROJECT_DIR/miniconda
+if ! [ -x "$(command -v conda)" ]; then
+  curl -L -o miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-$MINICONDA_VER-$tag-x86_64.sh
+  bash miniconda.sh -b -p $CI_PROJECT_DIR/miniconda
+fi
 
 export PATH=$CI_PROJECT_DIR/miniconda/bin:$PATH
 
@@ -17,6 +17,5 @@ conda config --system --add channels defaults
 conda config --system --add channels bioconda
 conda config --system --add channels conda-forge
 
-# After SSHing in, for some reason this seems to fix it...
 conda update -y conda
 conda create -n lcdb-wf-test -y --file requirements.txt

From f80cf9caf08f9c7d1d75af342f12454be2e6bcac Mon Sep 17 00:00:00 2001
From: Ryan Dale <dalerr@niddk.nih.gov>
Date: Sun, 14 Apr 2019 20:38:35 +0000
Subject: [PATCH 32/38] only do updates if not using cache

---
 .circleci/setup.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.circleci/setup.sh b/.circleci/setup.sh
index 944a1954a..37b2d0b4c 100755
--- a/.circleci/setup.sh
+++ b/.circleci/setup.sh
@@ -4,11 +4,12 @@ set -e
 MINICONDA_VER=latest
 tag="Linux"
 
-apt-get update
-apt-get install -y curl
 if ! [ -x "$(command -v conda)" ]; then
+  apt-get update
+  apt-get install -y curl
   curl -L -o miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-$MINICONDA_VER-$tag-x86_64.sh
   bash miniconda.sh -b -p $CI_PROJECT_DIR/miniconda
+  conda update -y conda
 fi
 
 export PATH=$CI_PROJECT_DIR/miniconda/bin:$PATH
@@ -17,5 +18,4 @@ conda config --system --add channels defaults
 conda config --system --add channels bioconda
 conda config --system --add channels conda-forge
 
-conda update -y conda
 conda create -n lcdb-wf-test -y --file requirements.txt

From 431017b4aa0c5934a5a41785f82d9d36823e7137 Mon Sep 17 00:00:00 2001
From: Ryan Dale <dalerr@niddk.nih.gov>
Date: Sun, 14 Apr 2019 20:47:28 +0000
Subject: [PATCH 33/38] only install if not cached

---
 .circleci/setup.sh | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.circleci/setup.sh b/.circleci/setup.sh
index 37b2d0b4c..aba20c175 100755
--- a/.circleci/setup.sh
+++ b/.circleci/setup.sh
@@ -10,12 +10,13 @@ if ! [ -x "$(command -v conda)" ]; then
   curl -L -o miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-$MINICONDA_VER-$tag-x86_64.sh
   bash miniconda.sh -b -p $CI_PROJECT_DIR/miniconda
   conda update -y conda
-fi
+  export PATH=$CI_PROJECT_DIR/miniconda/bin:$PATH
+
 
-export PATH=$CI_PROJECT_DIR/miniconda/bin:$PATH
+  conda create -n lcdb-wf-test -y --file requirements.txt
+fi
 
 conda config --system --add channels defaults
 conda config --system --add channels bioconda
 conda config --system --add channels conda-forge
 
-conda create -n lcdb-wf-test -y --file requirements.txt

From f26e90753ad91dff81e80a176f87e1820df7d079 Mon Sep 17 00:00:00 2001
From: Ryan Dale <dalerr@niddk.nih.gov>
Date: Mon, 15 Apr 2019 19:31:34 +0000
Subject: [PATCH 34/38] minor

---
 .gitlab-ci.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7bafe13d1..c23d731c7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -29,4 +29,3 @@ run-chipseq:
     paths:
       - "$CI_PROJECT_DIR/miniconda/"
     policy: "pull"
-

From 80122fde252af782ac71b8f8d9000f8256f89eee Mon Sep 17 00:00:00 2001
From: Ryan Dale <dalerr@niddk.nih.gov>
Date: Mon, 15 Apr 2019 20:07:59 +0000
Subject: [PATCH 35/38] export env.yaml as artifact

---
 .gitlab-ci.yml | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c23d731c7..e343b30ee 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -8,22 +8,26 @@ before_script:
 initialize-conda:
   stage: "init"
   image: "ubuntu:latest"
-  script: "bash .circleci/setup.sh"
+  script:
+    - "bash .circleci/setup.sh"
+    - "conda env export -n lcdb-wf > env.yaml"
   cache:
     key: "v1"
     paths:
       - "$CI_PROJECT_DIR/miniconda/"
+  artifact:
+    paths:
+      - '$CI_PROJECT_DIR/env.yaml'
+
 
 run-chipseq:
   stage: "workflows"
   image: "ubuntu:latest"
   script:
-    - echo $PATH
-    - which conda
     - source activate lcdb-wf-test
     - python ci/get-data.py
     - cd workflows/chipseq
-    - ./run_test.sh -n
+    - ./run_test.sh --use-conda -j8 -k -p -r
   cache:
     key: "v1"
     paths:

From 1eaaa6eceb1a297774fb605cf39d81d8d94fc92e Mon Sep 17 00:00:00 2001
From: Ryan Dale <dalerr@niddk.nih.gov>
Date: Mon, 15 Apr 2019 20:11:29 +0000
Subject: [PATCH 36/38] export env.yaml as artifact

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index e343b30ee..f3059415a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -15,7 +15,7 @@ initialize-conda:
     key: "v1"
     paths:
       - "$CI_PROJECT_DIR/miniconda/"
-  artifact:
+  artifacts:
     paths:
       - '$CI_PROJECT_DIR/env.yaml'
 

From 45dfc67811c18e9935e79e5acb065e179b3a1f8d Mon Sep 17 00:00:00 2001
From: Ryan Dale <dalerr@niddk.nih.gov>
Date: Sat, 20 Apr 2019 20:30:31 +0000
Subject: [PATCH 37/38] support chipseq paired end

---
 lib/patterns_targets.py                        | 1 +
 workflows/chipseq/config/chipseq_patterns.yaml | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/lib/patterns_targets.py b/lib/patterns_targets.py
index 643d8316a..0b837932f 100644
--- a/lib/patterns_targets.py
+++ b/lib/patterns_targets.py
@@ -161,6 +161,7 @@ def __init__(self, config, patterns, workdir=None):
         # First, the samples...
         self.patterns_by_sample = self.patterns['patterns_by_sample']
         self.fill_by_sample = dict(
+            n=[1,2],
             sample=self.samples.values,
             label=self.sampletable.label.values,
             ip_label=self.sampletable.label[
diff --git a/workflows/chipseq/config/chipseq_patterns.yaml b/workflows/chipseq/config/chipseq_patterns.yaml
index 94130b546..1e7a4fd63 100644
--- a/workflows/chipseq/config/chipseq_patterns.yaml
+++ b/workflows/chipseq/config/chipseq_patterns.yaml
@@ -1,7 +1,7 @@
 patterns_by_sample:
 
-  fastq: 'data/chipseq_samples/{sample}/{sample}_R1.fastq.gz'
-  cutadapt: 'data/chipseq_samples/{sample}/{sample}_R1.cutadapt.fastq.gz'
+  fastq: 'data/chipseq_samples/{sample}/{sample}_R{n}.fastq.gz'
+  cutadapt: 'data/chipseq_samples/{sample}/{sample}_R{n}.cutadapt.fastq.gz'
   bam: 'data/chipseq_samples/{sample}/{sample}.cutadapt.bam'
 
   fastqc:

From 82f84ace6b2e94c4bdf4f94784f035be98db7bd0 Mon Sep 17 00:00:00 2001
From: Ryan Dale <dalerr@niddk.nih.gov>
Date: Sat, 20 Apr 2019 20:40:09 +0000
Subject: [PATCH 38/38] export correct env

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f3059415a..ef2b1ab77 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -10,7 +10,7 @@ initialize-conda:
   image: "ubuntu:latest"
   script:
     - "bash .circleci/setup.sh"
-    - "conda env export -n lcdb-wf > env.yaml"
+    - "conda env export -n lcdb-wf-test > env.yaml"
   cache:
     key: "v1"
     paths: