changeset 127:d8baf7dafbd8 draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit dfe15e79689bca8ddcd843f9cf47eff29f6ee2e4-dirty
author ximgchess
date Thu, 15 Jun 2023 19:08:58 +0000
parents ca285a3cc30b
children 0823bbfb0a78
files chap/chap.xml inference/chapmlaas.xml macros.xml saxswaxs/PIL5.poni saxswaxs/PIL5.tif saxswaxs/pipeline.yaml saxswaxs/reduce.xml saxswaxs/test_1d saxswaxs/test_1d_001/test_1d_PIL11_001_000.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_001.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_002.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_003.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_004.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_005.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_006.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_007.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_008.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_009.tiff saxswaxs/test_1d_001/test_1d_PIL11_001_010.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_000.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_001.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_002.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_003.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_004.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_005.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_006.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_007.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_008.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_009.tiff saxswaxs/test_1d_001/test_1d_PIL5_001_010.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_000.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_001.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_002.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_003.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_004.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_005.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_006.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_007.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_008.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_009.tiff saxswaxs/test_1d_001/test_1d_PIL9_001_010.tiff tomo/test.txt tomo/tmp.txt tomo/tomo_macros.xml
diffstat 44 files changed, 145 insertions(+), 92 deletions(-) [+]
line wrap: on
line diff
--- a/chap/chap.xml	Tue May 30 18:03:00 2023 +0000
+++ b/chap/chap.xml	Thu Jun 15 19:08:58 2023 +0000
@@ -1,6 +1,9 @@
 <tool id="CHAP_test" name="CHESS Analysis Pipeline" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
+    <macros>
+        <import>../macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="0.0.2">ChessAnalysisPipeline</requirement>
+        <expand macro="chap-requirement" />
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         cp '$input' data.csv &&
@@ -29,14 +32,6 @@
         required configuration pipeline and necessary data.
     ]]></help>
     <citations>
-        <citation type="bibtex">
-@misc{githubChessAnalysisPipeline,
-  author = {LastTODO, FirstTODO},
-  year = {TODO},
-  title = {ChessAnalysisPipeline},
-  publisher = {GitHub},
-  journal = {GitHub repository},
-  url = {https://github.com/CHESSComputing/ChessAnalysisPipeline},
-}</citation>
+        <expand macro="chap-citation" />
     </citations>
 </tool>
--- a/inference/chapmlaas.xml	Tue May 30 18:03:00 2023 +0000
+++ b/inference/chapmlaas.xml	Thu Jun 15 19:08:58 2023 +0000
@@ -1,7 +1,10 @@
 <tool id="CHAP_inference_demo" name="CHAP MLaaS" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
+    <macros>
+        <import>../macros.xml</import>
+    </macros>
     <requirements>
         <requirement type="package" version="2.28.2">requests</requirement>
-        <requirement type="package" version="0.0.2">chessanalysispipeline</requirement>
+	<expand macro="chap-requirement" />
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         cp '$input' data.csv &&
@@ -46,14 +49,6 @@
 
     ]]></help>
     <citations>
-        <citation type="bibtex">
-@misc{githubChessAnalysisPipeline,
-  author = {Kuznetsov, Valentin},
-  year = {2023},
-  title = {ChessAnalysisPipeline},
-  publisher = {GitHub},
-  journal = {GitHub repository},
-  url = {https://github.com/CHESSComputing/ChessAnalysisPipeline},
-}</citation>
+        <expand macro="chap-citation" />
     </citations>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jun 15 19:08:58 2023 +0000
@@ -0,0 +1,8 @@
+<macros>
+  <xml name="chap-requirement">
+    <requirement type="package" version="PACKAGE_VERSION">chessanalysispipeline</requirement>
+  </xml>
+  <xml name="chap-citation">
+    <citation type="doi">10.5281/zenodo.7963532</citation>
+  </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/saxswaxs/PIL5.poni	Thu Jun 15 19:08:58 2023 +0000
@@ -0,0 +1,12 @@
+# Nota: C-Order, 1 refers to the Y axis, 2 to the X axis 
+# Calibration done at Wed Dec  1 09:43:02 2021
+poni_version: 2
+Detector: Pilatus300k
+Detector_config: {}
+Distance: 1.6482087488134558
+Poni1: 0.1678687786895594
+Poni2: 0.13236163515363114
+Rot1: 0.05582857735072926
+Rot2: -0.07300334677284326
+Rot3: 3.757385675073369e-05
+Wavelength: 1.2781876020248165e-10
Binary file saxswaxs/PIL5.tif has changed
--- a/saxswaxs/pipeline.yaml	Tue May 30 18:03:00 2023 +0000
+++ b/saxswaxs/pipeline.yaml	Thu Jun 15 19:08:58 2023 +0000
@@ -1,6 +1,6 @@
 pipeline:
 
-  # Integrate map detetcor data
+  # Integrate map detector data
   - pipeline.MultiplePipelineItem:
       items:
         - common.YAMLReader:
--- a/saxswaxs/reduce.xml	Tue May 30 18:03:00 2023 +0000
+++ b/saxswaxs/reduce.xml	Thu Jun 15 19:08:58 2023 +0000
@@ -1,6 +1,9 @@
 <tool id="CHAP_saxswaxs_reduce" name="SAXSWAXS Reduce Map" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
+    <macros>
+      <import>../macros.xml</import>
+    </macros>
     <requirements>
-      <requirement type="package" version="0.0.8">chessanalysispipeline</requirement>
+      <expand macro="chap-requirement" />
       <requirement type="package" version="1.0.1">nexusformat</requirement>
       <requirement type="package" version="2023.3.0">pyfai</requirement>
       <requirement type="package" version="1.10.7">pydantic</requirement>
@@ -35,14 +38,6 @@
 
     ]]></help>
     <citations>
-        <citation type="bibtex">
-@misc{githubChessAnalysisPipeline,
-  author = {LastTODO, FirstTODO},
-  year = {TODO},
-  title = {CHAPSAXSWAXSdemo},
-  publisher = {GitHub},
-  journal = {GitHub repository},
-  url = {https://github.com/CHESSComputing/ChessAnalysisPipeline},
-}</citation>
+        <expand macro="chap-citation" />
     </citations>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/saxswaxs/test_1d	Thu Jun 15 19:08:58 2023 +0000
@@ -0,0 +1,92 @@
+#F sample_14_align
+#E 1637195555
+#D Wed Nov 17 19:32:35 2021
+#C spec  User = chess_id3b
+
+#O0 mono  monz  mchi  mony  monx  und_CL  s0s  s0n
+#O1 s0t  s0b  s0x  s0h  s0z  s0v  mirzu  mirzd
+#O2 mirbu  mirbd  xu  yu  zu  xd  zld  zrd
+#O3 fpx  att  mirz  mirth  s3b  s3t  s3s  s3n
+#O4 s3z  s3v  s3x  s3h  s1b  s1t  s1s  s1n
+#O5 s1z  s1v  s1x  s1h  fl1x  fl1z  fl2x  fl2z
+#O6 waxx  waxz1  waxz2  waxz  waxtilt  xmirx  xmirz  xmirphi
+#O7 xmirth  saxx  saxy  saxz  andy  andz  zl2  xl2
+#O8 yl2  yr2  zru2  zrd2  xd7  zd7  xu7  zu7
+#O9 bedx_lo  icvx  icvz  air_x  p3y  p3z  nozx  nozz
+#O10 bedx  bedx_galil  s2b  s2t  s2s  s2n  s2z  s2v
+#O11 s2x  s2h  xrfx  xrfy  xrfz  zd5  zru5  zlu5
+#O12 yd5  xd5  xu5  tabx5  zr6  zlu6  zld6  yr6
+#O13 yl6  xr6  th  tth  phi  vtxx  txr  tyr
+#O14 tzr  txt  tyt  tzt  txr2  tyr2  tzr2  txt2
+#O15 tyt2  tzt2  txr3  tyr3  tzr3  txt3  tyt3  tzt3
+#O16 txr4  tyr4  tzr4  txt4  tyt4  tzt4  txr5  tyr5
+#O17 tzr5  txt5  tyt5  tzt5  txr6  tyr6  tzr6  txt6
+#O18 tyt6  tzt6  txr7  tyr7  tzr7  txt7  tyt7  tzt7
+#O19 txr8  tyr8  tzr8  txt8  tyt8  tzt8  
+#o0 mono monz mchi mony monx und s0s s0n
+#o1 s0t s0b s0x s0h s0z s0v mirzu mirzd
+#o2 mirbu mirbd xu yu zu xd zld zrd
+#o3 fpx att mirz mirth s3b s3t s3s s3n
+#o4 s3z s3v s3x s3h s1b s1t s1s s1n
+#o5 s1z s1v s1x s1h fl1x fl1z fl2x fl2z
+#o6 waxx waxz1 waxz2 waxz waxtilt xmirx xmirz xmirphi
+#o7 xmirth saxx saxy saxz andy andz zl2 xl2
+#o8 yl2 yr2 zru2 zrd2 xd7 zd7 xu7 zu7
+#o9 bedx_lo icvx icvz air_x p3y p3z nozx nozz
+#o10 bedx bedx_g s2b s2t s2s s2n s2z s2v
+#o11 s2x s2h samx samy samz zd5 zru5 zlu5
+#o12 yd5 xd5 xu5 tabx5 zr6 zlu6 zld6 yr6
+#o13 yl6 xr6 th tth phi vtxx txr tyr
+#o14 tzr txt tyt tzt txr2 tyr2 tzr2 txt2
+#o15 tyt2 tzt2 txr3 tyr3 tzr3 txt3 tyt3 tabz
+#o16 txr4 tyr4 tzr4 txt4 tyt4 tzt4 txr5 tyr5
+#o17 tzr5 txt5 tyt5 tzt5 txr6 tyr6 tzr6 txt6
+#o18 tyt6 tzt6 txr7 tyr7 tzr7 crlx tyt7 crlz
+#o19 txr8 tyr8 tzr8 txt8 bedy bedz 
+#J0 Seconds  ic0_ni  keyz  icv_pos  icv_sum  tminus  sec_2  diode
+#J1 ic1  ic3  icv_lo  icv_hi  mot_pulse  p11_r1  
+#j0 sec ic0_ni keyz icv_pos icv_sum tminus sec_2 diode
+#j1 ic1 ic3 icv_lo icv_hi pulses p11_r1 
+
+
+#S 1  flyscan samx 140.9 141.5 10 0.1 
+#D Wed Nov 17 19:35:47 2021
+#T 12  (Seconds)
+#G0 0
+#G1 0
+#G3 0
+#G4 0
+#Q 
+#P0 -3.7830971 3.0011801 -0.22821594 -3.8 13.94 3.69 34.924802 35.874722
+#P1 20.129699 18.629511 35.399834 0.94995949 19.379555 1.5001232 9.3153197 6.2847224
+#P2 7.6113723e-07 -3.039743e-07 3.4829819 1.005207 -9.6873251 -4.7275845 -10.608966 -10.438151
+#P3 -10.972008 544.544 7.8 -3.4595 -0.004199987 0.34579999 1.76 2.1600002
+#P4 0.1708 0.35 1.96 0.4 -1.35 -0.85000006 -0.30000002 0.40000036
+#P5 -1.1 0.5 0.05 0.7 -1.5328934 -20.102657 -8.9922526 -3.4989075
+#P6 11.303603 27.619064 29.211176 28.415 0.796 -3.0517576e-08 0.058524542 3.516674e-09
+#P7 0.49999989 8 1 -6 170 5.1999999 -11.341377 -4.0548513
+#P8 0.91678883 0.91679319 -9.7110746 -7.5862294 1.1553852 -0.19508918 4.0468633 -0.2839906
+#P9 11.900876 0.13366788 2.9005861 -1.2465739 385.49999 70 -13.999995 9.9999998
+#P10 -4.3098231e-06 -174.51549 -1.2799991 -0.37999994 2.8299999 3.5300016 -0.83 0.9
+#P11 3.18 0.7 140.8975 26.999999 141.6 1.0000013 4.0000013 4.0000013
+#P12 6.8038999 -0.59999922 -0.59999922 292 -20.93269 -45.083693 -11.619761 4.6857093e-09
+#P13 1.5745194e-08 -8.0676912 8.5449218e-08 90 0 9.1661255e-07 -1.1665 0.3365
+#P14 11.4515 -0.4805 1.496 -10.1055 4.183 3.7555 0 -2.5
+#P15 -0.815 -9.995 -0.0065 -0.081 -9 14.9515 0.0045 -0.4
+#P16 9.228 -1.1635 -9.65 0.4 -4.3845 1.0185 -2.201 0
+#P17 0 -0.6 8.1215 2.5 55.4955 5.769 0 -4.1045
+#P18 -38.1255 -24.9045 0.234 0.234 7.609 1.2315 0.234 -0.1975
+#P19 -10.2505 -10.2505 -0.6675 -10.2505 0 0 
+#N 9
+#L xrfx  Seconds  sec_2  diode  ic1  ic3  icv_lo  icv_hi  mot_pulse  
+140.899995 0 0.302713 10898.0 14772.0 29927.0 93811.0 87169.0 0
+140.959995 0 0.100783 3615.0 4910.0 9950.0 30648.0 29072.0 0
+141.019995 0 0.099614 3592.0 4902.0 9951.0 30359.0 28781.0 0
+141.079995 0 0.099614 1264.0 4851.0 9819.0 30288.0 28727.0 0
+141.139995 0 0.099614 877.0 4709.0 9445.0 30411.0 28511.0 0
+141.199995 0 0.100398 631.0 4764.0 9537.0 30308.0 28751.0 0
+141.259995 0 0.100782 542.0 4804.0 9630.0 30359.0 28916.0 0
+141.319995 0 0.099614 625.0 4839.0 9743.0 30425.0 28762.0 0
+141.379995 0 0.099614 542.0 4787.0 9597.0 30298.0 28635.0 0
+141.439995 0 0.099614 665.0 4784.0 9599.0 30283.0 28662.0 0
+141.499995 0 0.146491 1248.0 6957.0 13906.0 44347.0 42023.0 0
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--- a/tomo/test.txt	Tue May 30 18:03:00 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-I had a Galaxy tool crash repeatedly on Friday and tried a bunch of things, but nothing helped. Today I tried it from scratch and kept notes:
-
-Removed everything in:
- /nfs/chess/galaxy-dev/var/shed_tools/testtoolshed.g2.bx.psu.edu/repos/ximgchess
-and in:
-/nfs/chess/galaxy-dev/var/dependencies/_conda/envs
-
-Rebooted the ansible
-
-Made sure that the repo in the testtoolshed is up to date.
-
-Reinstall the CHAP tool at:
-https://galaxy-dev.classe.cornell.edu/admin/toolshed
-Watching its progress, I can see that it first clones the tool repo and then installs the tool dependencies.
-When done, I have the following new content in the galaxy tree:
-ls -al /nfs/chess/galaxy-dev/var/dependencies/_conda/envs:
-drwxr-xr-x 3 galaxy galaxy 32 May  1 09:17 .
-drwxr-xr-x 5 galaxy galaxy 52 Apr 28 08:40 ..
-drwxr-xr-x 3 galaxy galaxy 26 May  1 09:18 chap_test_20230411
-
-ls -al /nfs/chess/galaxy-dev/var/shed_tools/testtoolshed.g2.bx.psu.edu/repos/ximgchess:
-drwxr-xr-x  6 galaxy galaxy  317 May  1 10:04 .
-drwxr-xr-x 15 galaxy galaxy  226 Aug 29  2021 ..
-drwxr-xr-x 12 galaxy galaxy  184 May  1 10:03 __ChessAnalysisPipeline@0.0.2
--rw-r--r--  1 galaxy galaxy    0 May  1 09:18 .conda_envs_dir_test
-drwxr-xr-x 27 galaxy galaxy 4096 May  1 10:02 mulled-v1-0cd3a5ccc731743d38833d0396752d8219d106c20bb3bb478c34e74608ecb1c3
-drwxr-xr-x 26 galaxy galaxy 4096 May  1 09:51 mulled-v1-67ac3841866ce74ad34393f2abb6cc61f6651a9d3f3e677b9821c88c9b0a676e
-drwxr-xr-x 12 galaxy galaxy  184 May  1 10:04 mulled-v1-b1085bc9e4a5d280004f5b197e8295b3ef5167ea9ea22a074defb863f1b86458
-
-When running a Galaxy tool and only when I try to pip install certif-pyspec, it bombs with:
-OSError: [Errno 30] Read-only file system: '__config__.cpython-310.pyc'
-
-See stdout and stderr in:
-/nfs/chess/aux/reduced_data/user/galaxy-dev/jobs/002/2440/outputs
--- a/tomo/tmp.txt	Tue May 30 18:03:00 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-try:
-    from pyspec.file.spec import FileSpec
-    from pyspec.file.tiff import TiffFile
-except:
-    import sys
-    home = '/home/galaxy'
-    localpippath = f'{home}/.local/lib/python3.11/site-packages'
-    if localpippath not in sys.path:
-        sys.path.insert(0, localpippath)
-    from pyspec.file.spec import FileSpec
-    from pyspec.file.tiff import TiffFile
-
-
--- a/tomo/tomo_macros.xml	Tue May 30 18:03:00 2023 +0000
+++ b/tomo/tomo_macros.xml	Thu Jun 15 19:08:58 2023 +0000
@@ -1,10 +1,12 @@
 <macros>
+    <import>../macros.xml</import>
     <token name="@TOOL_VERSION@">0.1.0</token>
     <token name="@PROFILE@">21.09</token>
     <token name="@PYTHON_TEMPLATE_VERSION@">3.11</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.0.8">chessanalysispipeline</requirement>
+	    <expand macro="chap-requirement" />
+            <!-- <requirement type="package" version="0.0.8">chessanalysispipeline</requirement> -->
             <requirement type="package" version="1.1.0">lmfit</requirement>
             <requirement type="package" version="3.7.1">matplotlib</requirement>
             <requirement type="package" version="1.0.1">nexusformat</requirement>
@@ -14,19 +16,20 @@
     </xml>
     <xml name="citations">
         <citations>
-            <citation type="bibtex">
-@software{keara_soloway_2023_7963605,
-  author       = {Keara Soloway and
-                  Valentin Kuznetsov and
-                  Rolf Verberg},
-  title        = {CHESSComputing/ChessAnalysisPipeline: v0.0.8},
-  month        = may,
-  year         = 2023,
-  publisher    = {Zenodo},
-  version      = {v0.0.8},
-  doi          = {10.5281/zenodo.7963605},
-  url          = {https://doi.org/10.5281/zenodo.7963605}
-}</citation>
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+<!--   author       = {Keara Soloway and -->
+<!--                   Valentin Kuznetsov and -->
+<!--                   Rolf Verberg}, -->
+<!--   title        = {CHESSComputing/ChessAnalysisPipeline: v0.0.8}, -->
+<!--   month        = may, -->
+<!--   year         = 2023, -->
+<!--   publisher    = {Zenodo}, -->
+<!--   version      = {v0.0.8}, -->
+<!--   doi          = {10.5281/zenodo.7963605}, -->
+<!--   url          = {https://doi.org/10.5281/zenodo.7963605} -->
+<!-- }</citation> -->
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