Merge pull request #70 from abkfenris/julia-tutorial

Julia's tutorial

Author: abkfenris

py-base/conda-linux-64.lock

@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 524d906548a29041e55434347d2b89debfa2e3506deef00fa92de98daf81210a
+# input_hash: 73a1fd52890a92f967bc7d061910a6efeed97e5553a6440a21ca4a8b93aee663
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2
@@ -92,6 +92,7 @@ https://conda.anaconda.org/conda-forge/linux-64/rdma-core-28.9-h59595ed_1.conda#
 https://conda.anaconda.org/conda-forge/linux-64/re2-2023.03.02-h8c504da_0.conda#206f8fa808748f6e90599c3368a1114e
 https://conda.anaconda.org/conda-forge/linux-64/reproc-14.2.4-h0b41bf4_0.conda#0f51393e019df1f0047ef864cd9ddeec
 https://conda.anaconda.org/conda-forge/linux-64/snappy-1.1.10-h9fff704_0.conda#e6d228cd0bb74a51dd18f5bfce0b4115
+https://conda.anaconda.org/bioconda/linux-64/sra-tools-2.9.6-hf484d3e_0.tar.bz2#010360b3ab732be603d3798b5d1bacc4
 https://conda.anaconda.org/conda-forge/linux-64/svt-av1-1.6.0-h59595ed_0.conda#26d28bba29ad67e81fa278b417f7e00a
 https://conda.anaconda.org/conda-forge/linux-64/tzcode-2023c-h0b41bf4_0.conda#0c0533894f21c3d35697cb8378d390e2
 https://conda.anaconda.org/conda-forge/linux-64/unzip-6.0-h7f98852_3.tar.bz2#7cb7109505433a5abbf68bb34b31edac
@@ -178,7 +179,9 @@ https://conda.anaconda.org/conda-forge/linux-64/mpc-1.3.1-hfe3b2da_0.conda#289c7
 https://conda.anaconda.org/conda-forge/linux-64/nss-3.89-he45b914_0.conda#2745719a58eeaab6657256a3f142f099
 https://conda.anaconda.org/conda-forge/linux-64/orc-1.9.0-h385abfd_1.conda#2cd5aac7ef1b4c6ac51bf521251a89b3
 https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.1.3-h32600fe_0.conda#8287aeb8462e2d4b235eff788e75919d
+https://conda.anaconda.org/conda-forge/linux-64/pigz-2.6-h27826a3_0.tar.bz2#677798489006b14291e8617223e34348
 https://conda.anaconda.org/conda-forge/linux-64/python-3.9.16-h2782a2a_0_cpython.conda#95c9b7c96a7fd7342e0c9d0a917b8f78
+https://conda.anaconda.org/bioconda/linux-64/seqtk-1.4-he4a0461_1.tar.bz2#6171aed4c1ca97a5d34e3bcad7bee3f4
 https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.42.0-h2c6b66d_0.conda#1192f6ec654a5bc4ee1d64bdc4a3e5cc
 https://conda.anaconda.org/conda-forge/linux-64/udunits2-2.2.28-hc3e0081_0.tar.bz2#d4c341e0379c31e9e781d4f204726867
 https://conda.anaconda.org/conda-forge/linux-64/wget-1.20.3-ha35d2d1_1.tar.bz2#c990e108f39e1b43adf61e984360c9a1
@@ -245,6 +248,7 @@ https://conda.anaconda.org/conda-forge/linux-64/gts-0.7.6-h977cf35_4.conda#4d8df
 https://conda.anaconda.org/conda-forge/linux-64/gxx-12.3.0-h8d2909c_1.conda#52061516ce5d0aebb4282f72ef2347e5
 https://conda.anaconda.org/conda-forge/linux-64/gxx_linux-64-12.3.0-h8a814eb_1.conda#6445e3f748b36c1b361f0def984d1763
 https://conda.anaconda.org/conda-forge/noarch/hpack-4.0.0-pyh9f0ad1d_0.tar.bz2#914d6646c4dbb1fd3ff539830a12fd71
+https://conda.anaconda.org/conda-forge/linux-64/humanfriendly-10.0-py39hf3d152e_4.tar.bz2#3844897723d78cca5f813ad6bee5fc7b
 https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.0.1-pyhd8ed1ab_0.tar.bz2#9f765cbfab6870c8435b9eefecd7a1f4
 https://conda.anaconda.org/conda-forge/noarch/idna-3.4-pyhd8ed1ab_0.tar.bz2#34272b248891bddccc64479f9a7fffed
 https://conda.anaconda.org/conda-forge/noarch/iniconfig-2.0.0-pyhd8ed1ab_0.conda#f800d2da156d08e289b14e87e43c1ae5
@@ -342,6 +346,7 @@ https://conda.anaconda.org/conda-forge/noarch/typing_utils-0.1.0-pyhd8ed1ab_0.ta
 https://conda.anaconda.org/conda-forge/noarch/uc-micro-py-1.0.1-pyhd8ed1ab_0.tar.bz2#3ddf6684d9b274a12c94e509ca45656c
 https://conda.anaconda.org/conda-forge/linux-64/unicodedata2-15.0.0-py39hb9d737c_0.tar.bz2#230d65004135bf312504a1bbcb0c7a08
 https://conda.anaconda.org/conda-forge/noarch/uri-template-1.3.0-pyhd8ed1ab_0.conda#0944dc65cb4a9b5b68522c3bb585d41c
+https://conda.anaconda.org/conda-forge/noarch/verboselogs-1.7-py_0.tar.bz2#ffce1c9059a29251d27b0075c41d83f3
 https://conda.anaconda.org/conda-forge/noarch/webcolors-1.13-pyhd8ed1ab_0.conda#166212fe82dad8735550030488a01d03
 https://conda.anaconda.org/conda-forge/noarch/webencodings-0.5.1-py_1.tar.bz2#3563be4c5611a44210d9ba0c16113136
 https://conda.anaconda.org/conda-forge/noarch/websocket-client-1.6.1-pyhd8ed1ab_0.conda#c34d9325a609381a0b0e8a5b4f325147
@@ -372,10 +377,11 @@ https://conda.anaconda.org/conda-forge/linux-64/cairo-1.16.0-hbbf8b49_1016.conda
 https://conda.anaconda.org/conda-forge/linux-64/cffi-1.15.1-py39he91dace_3.conda#20080319ef73fbad74dcd6d62f2a3ffe
 https://conda.anaconda.org/conda-forge/linux-64/cfitsio-4.2.0-hd9d235c_0.conda#8c57a9adbafd87f5eff842abde599cb4
 https://conda.anaconda.org/conda-forge/linux-64/cftime-1.6.2-py39h2ae25f5_1.tar.bz2#c943fb9a2818ecc5be1e0ecc8b7738f1
-https://conda.anaconda.org/conda-forge/noarch/click-default-group-1.2.2-pyhd8ed1ab_1.tar.bz2#72a46ffc25701c173932fd55cf0965d3
+https://conda.anaconda.org/conda-forge/noarch/click-default-group-1.2.3-pyhd8ed1ab_0.conda#d541f74d40048cd24506d1730b67d147
 https://conda.anaconda.org/conda-forge/noarch/click-plugins-1.1.1-py_0.tar.bz2#4fd2c6b53934bd7d96d1f3fdaf99b79f
 https://conda.anaconda.org/conda-forge/noarch/cligj-0.7.2-pyhd8ed1ab_1.tar.bz2#a29b7c141d6b2de4bb67788a5f107734
 https://conda.anaconda.org/conda-forge/noarch/clikit-0.6.2-pyhd8ed1ab_2.conda#02abb7b66b02e8b9f5a9b05454400087
+https://conda.anaconda.org/conda-forge/noarch/coloredlogs-15.0.1-pyhd8ed1ab_3.tar.bz2#7b4fc18b7f66382257c45424eaf81935
 https://conda.anaconda.org/conda-forge/noarch/colorspacious-1.1.2-pyh24bf2e0_0.tar.bz2#b73afa0d009a51cabd3ec99c4d2ef4f3
 https://conda.anaconda.org/conda-forge/noarch/comm-0.1.4-pyhd8ed1ab_0.conda#c8eaca39e2b6abae1fc96acc929ae939
 https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.1.0-py39h7633fee_0.conda#54e6f32e448fdc273606011f0940d076
@@ -421,6 +427,7 @@ https://conda.anaconda.org/conda-forge/noarch/pexpect-4.8.0-pyh1a96a4e_2.tar.bz2
 https://conda.anaconda.org/conda-forge/linux-64/pillow-10.0.0-py39haaeba84_0.conda#f97a95fab7c69678ebf6b57396b1323e
 https://conda.anaconda.org/conda-forge/linux-64/postgresql-15.3-h8972f4a_2.conda#7b78c6b8a755d4cb03f65ac3f664aed3
 https://conda.anaconda.org/conda-forge/linux-64/proj-9.2.1-ha643af7_0.conda#e992387307f4403ba0ec07d009032550
+https://conda.anaconda.org/conda-forge/noarch/property-manager-3.0-py_0.tar.bz2#a6da492df105d85ec943b99db66c02b1
 https://conda.anaconda.org/conda-forge/linux-64/protobuf-4.23.3-py39h45438f2_0.conda#b9bc216265605297ba37c39849e8b633
 https://conda.anaconda.org/conda-forge/noarch/pyasn1-modules-0.2.7-py_0.tar.bz2#ad1e886d09700b2304975335f714bd9c
 https://conda.anaconda.org/conda-forge/noarch/pyct-core-0.4.6-py_0.tar.bz2#55ec526f95e0959de3f68bc6289a20da
@@ -459,6 +466,7 @@ https://conda.anaconda.org/conda-forge/linux-64/cf-units-3.2.0-py39h0f8d45d_0.co
 https://conda.anaconda.org/conda-forge/linux-64/compilers-1.6.0-ha770c72_0.conda#e2259de4640a51a28c21931ae98e4975
 https://conda.anaconda.org/conda-forge/linux-64/cryptography-41.0.2-py39hd4f0224_0.conda#693ff4fd70b760464f27a16e280e99f3
 https://conda.anaconda.org/conda-forge/noarch/datashape-0.5.4-py_1.tar.bz2#50ddfce434ea596fc4497085f403a9d5
+https://conda.anaconda.org/conda-forge/noarch/executor-23.2-pyhd3deb0d_0.tar.bz2#01570739b18f4c62f040308cdd6318ef
 https://conda.anaconda.org/conda-forge/noarch/fqdn-1.5.1-pyhd8ed1ab_0.tar.bz2#642d35437078749ef23a5dca2c9bb1f3
 https://conda.anaconda.org/conda-forge/linux-64/geotiff-1.7.1-h22adcc9_11.conda#514167b60f598eaed3f7a60e1dceb9ee
 https://conda.anaconda.org/conda-forge/linux-64/git-2.41.0-pl5321h86e50cf_0.conda#14f8341e26b274362b026bbdc72b14fb
@@ -474,6 +482,7 @@ https://conda.anaconda.org/conda-forge/noarch/importlib-resources-6.0.0-pyhd8ed1
 https://conda.anaconda.org/conda-forge/noarch/importlib_metadata-6.8.0-hd8ed1ab_0.conda#b279b07ce18058034e5b3606ba103a8b
 https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2023.7.1-pyhd8ed1ab_0.conda#7c27ea1bdbe520bb830dcadd59f55cbf
 https://conda.anaconda.org/conda-forge/noarch/jupyter_server_terminals-0.4.4-pyhd8ed1ab_1.conda#7c0965e1d4a0ee1529e8eaa03a78a5b3
+https://conda.anaconda.org/bioconda/linux-64/kaiju-1.9.2-h43eeafb_3.tar.bz2#af38a1c858610af80b81ba7fcaf8a5a1
 https://conda.anaconda.org/conda-forge/linux-64/kealib-1.5.1-h3e6883b_4.conda#ef5228158594262a8bc07a0c92a3ef5b
 https://conda.anaconda.org/conda-forge/linux-64/libmambapy-1.4.9-py39h78efd80_0.conda#ad495f7b8e9889417e55f82ca5ef6b05
 https://conda.anaconda.org/conda-forge/linux-64/libspatialite-5.0.1-hca56755_27.conda#918a735059cab21b96fc13a8d04fbcd8
@@ -563,6 +572,7 @@ https://conda.anaconda.org/conda-forge/noarch/cdsapi-0.6.1-pyhd8ed1ab_0.conda#45
 https://conda.anaconda.org/conda-forge/linux-64/conda-23.7.2-py39hf3d152e_0.conda#7795d77006f93448cafc2751b9658bcc
 https://conda.anaconda.org/conda-forge/noarch/dataretrieval-1.0.5-pyhd8ed1ab_0.conda#b5d26d1a6056ac2ead0618fa4eb11d5f
 https://conda.anaconda.org/conda-forge/noarch/ensureconda-1.4.3-pyhd8ed1ab_0.tar.bz2#c99ae3abf501990769047b4b40a98f17
+https://conda.anaconda.org/bioconda/noarch/fastq-dl-1.1.1-hdfd78af_0.tar.bz2#7db7ceb925d4fb3aa69da12d91fe298c
 https://conda.anaconda.org/conda-forge/noarch/folium-0.14.0-pyhd8ed1ab_0.conda#48c8bb19df0d0268f1a9d30ffc56c5b0
 https://conda.anaconda.org/conda-forge/noarch/gh-scoped-creds-4.1-pyhd8ed1ab_0.tar.bz2#726906d636cc2e711d79abd236ce441f
 https://conda.anaconda.org/conda-forge/noarch/google-auth-2.22.0-pyh1a96a4e_0.conda#5583192796d1ebcf39b1e3e0958aa259

py-base/environment.yml

@@ -1,6 +1,7 @@
 name: OHW-py
 channels:
   - conda-forge
+  - bioconda
 dependencies:
   # base
   - python=3.9
@@ -112,6 +113,13 @@ dependencies:
   # - xlrd  # deprecated, use openpyxl instead
   - zarr
   # Tutorial specific, may be dupes to make things explicit
+  - kaiju # 23-Julia
+  - scikit-learn # 23-Julia
+  - fastq-dl # 23-Julia
+  - seqtk # 23-Julia
+  - pandas # 23-Julia
+  - matplotlib-base # 23-Julia
+  - seaborn # 23-Julia
   - pandas # 23-Myranda
   - xarray # 23-Myranda
   - seaborn # 23-Myranda