Merge pull request miykael#97 from miykael/correct_datalad_parallelism

Corrects datalad get's command from `-J4` to `-J 4`

Author: miykael

Dockerfile

@@ -1,5 +1,5 @@
-# Generated by Neurodocker version 0.4.0.dev2
-# Timestamp: 2018-05-18 14:48:41 UTC
+# Generated by Neurodocker version 0.4.0
+# Timestamp: 2018-06-26 13:39:06 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -232,8 +232,8 @@ RUN echo '{ \
     \n          "nilearn", \
     \n          "datalad[full]", \
     \n          "nipy", \
-    \n          "nbval", \
-    \n          "duecredit" \
+    \n          "duecredit", \
+    \n          "nbval" \
     \n        ], \
     \n        "create_env": "neuro", \
     \n        "activate": true \

casts/nipype_tutorial_showcase.sh

@@ -55,7 +55,7 @@ run "%time preproc01.run('MultiProc', plugin_args={'n_procs': 5})"
 
 say "Investigate the output"
 show "Investigate the output"
-run "!tree preproc01 -I '*js|*json|*pklz|_report|*.dot|*html'"
+run "!tree preproc_flow -I '*js|*json|*pklz|_report|*.dot|*html'"
 
 say "Change the size of the smoothing kernel"
 show "Change the size of the smoothing kernel"

create_dockerfile.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-docker run --rm kaczmarj/neurodocker:master generate docker\
+docker run --rm kaczmarj/neurodocker:master generate docker \
            --base neurodebian:stretch-non-free \
            --pkg-manager apt \
            --install convert3d ants fsl gcc g++ graphviz tree \

docs/notebooks/basic_data_input.html

@@ -12835,7 +12835,7 @@ <h2 id="FreeSurferSource">FreeSurferSource<a class="anchor-link" href="#FreeSurf
 <div class="prompt input_prompt">In&nbsp;[&nbsp;]:</div>
 <div class="inner_cell">
     <div class="input_area">
-<div class=" highlight hl-ipython3"><pre><span></span><span class="o">!</span>datalad get -r -J4 /data/ds000114/derivatives/freesurfer/sub-01
+<div class=" highlight hl-ipython3"><pre><span></span><span class="o">!</span>datalad get -r -J 4 /data/ds000114/derivatives/freesurfer/sub-01
 </pre></div>
 
 </div>

docs/notebooks/example_normalize.html

@@ -11806,7 +11806,7 @@ <h2 id="Preparation">Preparation<a class="anchor-link" href="#Preparation">&#182
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span>%%bash
-datalad get -J4 /data/ds000114/derivatives/fmriprep/sub-0<span class="o">[</span><span class="m">2345789</span><span class="o">]</span>/anat/*h5
+datalad get -J 4 /data/ds000114/derivatives/fmriprep/sub-0<span class="o">[</span><span class="m">2345789</span><span class="o">]</span>/anat/*h5
 </pre></div>
 
 </div>

docs/notebooks/example_preprocessing.html

@@ -11812,7 +11812,7 @@ <h2 id="Preparation">Preparation<a class="anchor-link" href="#Preparation">&#182
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span>%%bash
-datalad get -J4 /data/ds000114/derivatives/fmriprep/sub-*/anat/*preproc.nii.gz <span class="se">\</span>
+datalad get -J 4 /data/ds000114/derivatives/fmriprep/sub-*/anat/*preproc.nii.gz <span class="se">\</span>
                 /data/ds000114/sub-*/ses-test/func/*fingerfootlips*
 </pre></div>
 

docs/notebooks/handson_preprocessing.html

@@ -11807,7 +11807,7 @@ <h2 id="Preparation">Preparation<a class="anchor-link" href="#Preparation">&#182
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span>%%bash
-datalad get -J4 /data/ds000114/sub-0<span class="o">[</span><span class="m">234789</span><span class="o">]</span>/ses-test/anat/sub-0<span class="o">[</span><span class="m">234789</span><span class="o">]</span>_ses-test_T1w.nii.gz <span class="se">\</span>
+datalad get -J 4 /data/ds000114/sub-0<span class="o">[</span><span class="m">234789</span><span class="o">]</span>/ses-test/anat/sub-0<span class="o">[</span><span class="m">234789</span><span class="o">]</span>_ses-test_T1w.nii.gz <span class="se">\</span>
                 /data/ds000114/sub-0<span class="o">[</span><span class="m">234789</span><span class="o">]</span>/ses-test/func/*fingerfootlips*
 </pre></div>
 

docs/notebooks/introduction_dataset.html

@@ -11896,7 +11896,7 @@ <h1 id="Tutorial-Dataset">Tutorial Dataset<a class="anchor-link" href="#Tutorial
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span>%%bash
 <span class="nb">cd</span> /data/ds000114
-datalad get -J4 /data/ds000114/derivatives/fmriprep/sub-*/anat/*preproc.nii.gz <span class="se">\</span>
+datalad get -J 4 /data/ds000114/derivatives/fmriprep/sub-*/anat/*preproc.nii.gz <span class="se">\</span>
                 /data/ds000114/sub-*/ses-test/func/*fingerfootlips*
 </pre></div>
 

notebooks/basic_data_input.ipynb

@@ -651,7 +651,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!datalad get -r -J4 /data/ds000114/derivatives/freesurfer/sub-01"
+    "!datalad get -r -J 4 /data/ds000114/derivatives/freesurfer/sub-01"
    ]
   },
   {

notebooks/example_normalize.ipynb

@@ -27,7 +27,7 @@
    "outputs": [],
    "source": [
     "%%bash\n",
-    "datalad get -J4 /data/ds000114/derivatives/fmriprep/sub-0[2345789]/anat/*h5"
+    "datalad get -J 4 /data/ds000114/derivatives/fmriprep/sub-0[2345789]/anat/*h5"
    ]
   },
   {

notebooks/example_preprocessing.ipynb

@@ -32,7 +32,7 @@
    "outputs": [],
    "source": [
     "%%bash\n",
-    "datalad get -J4 /data/ds000114/derivatives/fmriprep/sub-*/anat/*preproc.nii.gz \\\n",
+    "datalad get -J 4 /data/ds000114/derivatives/fmriprep/sub-*/anat/*preproc.nii.gz \\\n",
     "                /data/ds000114/sub-*/ses-test/func/*fingerfootlips*"
    ]
   },

notebooks/handson_preprocessing.ipynb

@@ -29,7 +29,7 @@
    "outputs": [],
    "source": [
     "%%bash\n",
-    "datalad get -J4 /data/ds000114/sub-0[234789]/ses-test/anat/sub-0[234789]_ses-test_T1w.nii.gz \\\n",
+    "datalad get -J 4 /data/ds000114/sub-0[234789]/ses-test/anat/sub-0[234789]_ses-test_T1w.nii.gz \\\n",
     "                /data/ds000114/sub-0[234789]/ses-test/func/*fingerfootlips*"
    ]
   },

notebooks/introduction_dataset.ipynb

@@ -68,7 +68,7 @@
    "source": [
     "%%bash\n",
     "cd /data/ds000114\n",
-    "datalad get -J4 /data/ds000114/derivatives/fmriprep/sub-*/anat/*preproc.nii.gz \\\n",
+    "datalad get -J 4 /data/ds000114/derivatives/fmriprep/sub-*/anat/*preproc.nii.gz \\\n",
     "                /data/ds000114/sub-*/ses-test/func/*fingerfootlips*"
    ]
   },