cloudspades install trial 2

qiita-spots · Jan 21, 2025 · 82535f3 · 82535f3
1 parent 1496edc
commit 82535f3
Showing 1 changed file with 9 additions and 9 deletions.
diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml
@@ -80,23 +80,23 @@ jobs:
           conda config --add channels bioconda
 
           # installing qtp-sequencing
-          conda create -q --yes -n qtp-sequencing python=3.6 pip pigz quast
-          conda activate qtp-sequencing
-          pip --quiet install https://github.com/qiita-spots/qtp-sequencing/archive/master.zip
-          export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
-          export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
-          configure_qtp_sequencing --env-script "source /home/runner/.profile; conda activate qtp-sequencing" --server-cert $QIITA_SERVER_CERT
+          # conda create -q --yes -n qtp-sequencing python=3.6 pip pigz quast
+          # conda activate qtp-sequencing
+          # pip --quiet install https://github.com/qiita-spots/qtp-sequencing/archive/master.zip
+          # export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
+          # export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
+          # configure_qtp_sequencing --env-script "source /home/runner/.profile; conda activate qtp-sequencing" --server-cert $QIITA_SERVER_CERT
 
-          conda deactivate
+          # conda deactivate
 
           # installing this plugin
           conda create -q --yes -n qp-spades python=3.11 cmake clang zlib flash # spades=3.15.4
           conda activate qp-spades
 
           # installing cloudspades
           wget https://github.com/ablab/spades/archive/refs/tags/cloudspades-0.1.tar.gz
-          tar -zxf cloudspades-0.1.tar.gz
-          cd cloudspades-0.1/assembler
+          tar zxvf cloudspades-0.1.tar.gz
+          cd spades-cloudspades-0.1/assembler/
           sh spades_compile.sh
           bin/spades.py --test